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PublishedSourceTitleCategoriesFocal TopicsExtract DataDocument LocationWatershed CodeAbstractKeyword Tags
2017Martin Liermann, George Pess, Mike McHenry, John McMillan, Mel Elofson, Todd Bennett, Raymond MosesRelocation and Recolonization of Coho Salmon in Two Tributaries to the Elwha River: Implications for Management and Monitoring, , , ,

In 2012 the lower of two Elwha River dams was breached, restoring access of anadromous salmonids to the middle Elwha River (between the two dams), including two distinct tributaries, Indian Creek and Little River. While comparable in size, Indian Creek is considerably less steep than Little River (mean slope of 1.0% versus 3.5%, respectively) and has a warmer stream temperature regime due to its source, Lake Sutherland. During and after breaching, Coho Salmon Oncorhynchus kisutch were relocated to these tributaries from lower Elwha River hatcheries (below the dams) to determine if individuals from a hatchery-dominated population would successfully spawn and seed the systems with juveniles and to assess differences in recolonization between the streams. Transplantation led to immediate spawning, which resulted in levels of smolt out-migrants per stream kilometer comparable with other established Coho Salmon populations in the Pacific Northwest. During the first 2 years of the relocation, redd densities in the two systems were similar but Indian Creek produced four to five times as many smolts per kilometer as Little River. In addition, fry out-migration occurred 2 to 4 weeks earlier in Indian Creek, as predicted by the warmer incubation temperatures. In the first years of the study, there was little evidence of natural colonization of the two tributaries by adults. However, in 2016 over half of the observed adults returning to the two tributaries were not transplanted, suggesting that the progeny from the transplanted fish were returning to their natal waters. This work demonstrates that transplanting hatchery dominated Coho Salmon adults into newly available habitat can result in immediate freshwater production that is comparable to other systems and that density and timing of juvenile out-migrants can differ dramatically based on the seeded habitat.

Coho Salmon, Oncorhynchus kisutch, Elwha River, Relocation, Recolonization, Monitoring, Management
2017Daniel J. Prince, Sean M. O’Rourke, Tasha Q. Thompson, Omar A. Ali, Hannah S. Lyman, Ismail K. Saglam, Thomas J. Hotaling, Adrian P. Spidle, Michael R. MillerThe evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation

The delineation of conservation units (CUs) is a challenging issue that has profound implications forminimizing the loss of biodiversity and ecosystem services. CU delineation typically seeks to prioritize evolutionary significance, and genetic methods play a pivotal role in the delineation process by quantifying overall differentiation between populations. Although CUs that primarily reflect overall genetic differentiation do protect adaptive differences between distant populations, they do not necessarily protect adaptive variation within highly connected populations. Advances in genomic methodology facilitate the characterization of adaptive genetic variation, but the potential utility of this information for CU delineation is unclear. We use genomic methods to investigate the evolutionary basis of premature migration in Pacific salmon, a complex behavioral and physiological phenotype that exists within highly connected populations and has experienced severe declines. Strikingly, we find that prematuremigration is associated with the same single locus across multiple populations in each of two different species. Patterns of variation at this locus suggest that the premature migration alleles arose froma single evolutionary eventwithin each species and were subsequently spread to distant populations through straying and positive selection. Our results reveal that complex adaptive variation can depend on rare mutational events at a single locus, demonstrate that CUs reflecting overall genetic differentiation can fail to protect evolutionarily significant variation that has substantial ecological and societal benefits, and suggest that a supplemental framework for protecting specific adaptive variation will sometimes be necessary to prevent the loss of significant biodiversity and ecosystem services.

Pacific salmon (Oncorhynchus spp.), conservation units (CUs), premature migration
2017Jerri Bartholomew, Sascha Hallett, Rich Holt, Julie Alexander, Stephen Atkinson, Ryan Craig, Amir Javaheri, Meghna Babar-SebensKlamath River Fish Health Studies: Salmon Disease Monitoring and Research. Oregon State University, BOR/USGS Interagency Agreement #R15PG00065 FY2016 April 01, 2016 – March 31, 2017 Annual Report, , , 180102

The myxozoan parasite Ceratonova shasta infects the intestine of salmonid fishes, which can lead to enteronecrosis and mortality. The parasite is endemic to the Pacific Northwest of North America and has been responsible for high mortality in juvenile salmon in the Klamath River basin. Ceratonova shasta cycles between two hosts and two spore stages: waterborne actinospores released from freshwater polychaete worms infect salmonids and develop into myxospores, which are then infectious to polychaetes. The Bartholomew Lab at Oregon State University has been monitoring the spatial and temporal abundance of the parasite in the Klamath River basin since 2006 using sentinel fish exposures, river water sampling, and polychaete sampling. This report describes monitoring studies conducted in 2016. Those data are informing several models being developed to better predict disease effects under various temperature and flow conditions.

Results from polychaete density and infection assays completed in 2016 were remarkably different from those obtained in previous years: Densities decreased at all monitoring sites following the high magnitude flow event in March 2016. Infection prevalence was generally low in 2016 (<1%) which is in contrast to levels observed in 2015 (>1%). However, by late spring (June), densities had begun to increase at river sites downstream IGD including the Seiad Valley and Orleans sites, which are not normally characterized by elevated densities prior to late summer. However, prevalence of infection was high in polychaetes at the Orleans site, resulting in estimates of 5,000-35,000 infected polychaetes m-2. We suggest that polychaetes displaced from reaches below Iron Gate dam during the high magnitude but short duration flood in March settled out at KOR resulting in the relatively high densities detected at this site.

Myxozoan parasite, Ceratonova shasta, Salmon,
2013Crystal Robinson, Quartz Valley Indian ReservationQuartz Valley Indian Reservation Water Quality Monitoring and Assessment Report 2013, 180102

This document describes the water quality monitoring performed during 2013 by the Quartz Valley Indian Reservation (QVIR) Environmental Department. Our work is funded by Federal grants from the U.S. Environmental Protection Agency (USEPA) and is intended to help fulfill intentions of the Clean Water Act. Our efforts are designed to monitor the health of our local water bodies and to help protect waters for a variety of beneficial uses.

The QVIR Environmental Department began the process of developing a Water Pollution Control Program in accordance with the Clean Water Act (CWA) in 2005. The Tribe set primary goals of ensuring salmonid spawning and rearing habitat, fishing, swimming, other wildlife habitat and cultural needs. The objective is to ensure these goals are met for the future protection and sustained use of valuable Reservation water resources, protection of public health and welfare, and the enhancement of water quality resources. The Tribe intends to protect and improve water resources through water quality monitoring, habitat evaluation, education and community outreach, planning and implementation.

A Quality Assurance Project Plan (QVIR 2006a) for water quality monitoring was developed by the Tribal Environmental Program and approved by U.S. Environmental Protection Agency (U.S. EPA) in 2006. Current water quality conditions are annually evaluated using the water quality objectives developed from various state, federal and tribal entities. The North Coast Regional Water Quality Control Board (NCRWQCB) Basin Plan water quality objectives are determined for the protection of beneficial uses (e.g., salmonids, agriculture, and recreation) established for the Scott River and its tributaries. U.S. EPA's (2000a)

Water Quality, Quartz Valley Indian Reservation (QVIR), Water Temperature,
2013Hoopa Tribal Environmental Protection Agency, Water Quality, Water Quality Monitoring by the Hoopa Tribal Environmental Protection Agency 2008–2012 PREPARED BY180102

This report presents the results of the Hoopa Tribal Environmental Protection Agency’s (Hoopa TEPA) water quality monitoring within the Hoopa Valley Indian Reservation for the years 2008 to 2012. Hoopa TEPA is a member of the Klamath Basin Tribal Water Quality Work Group (Work Group) and has worked to develop and implement shared water quality monitoring protocols with the Yurok Tribe and the Karuk Tribe who also conduct monitoring in the Trinity and Lower Klamath basins.

Samples were collected by Hoopa TEPA staff at two stations: the Klamath River at Saints Rest Bar and the Trinity River at Hoopa. The beginning and end of the sampling season varied by year, with samples collected from mid or late May through early or mid-October. Sampling frequency was generally monthly in 2008 and bi-weekly (every two weeks) in 2009-2012. Water samples were collected and analyzed for nutrients, chlorophyll-a, algal toxins, phytoplankton species (i.e., free-floating algae), and other chemical parameters. Periphyton samples (i.e., algae attached the riverbed) were collected by scraping a fixed area from river cobbles and then analyzed for chlorophyll-a and algal species. The laboratory analyses of the water and periphyton samples were performed using funds awarded to the Klamath Basin Tribal Water Quality Work Group by the U.S. EPA Region 9.

In the report, sampling results are compared with the water quality standards from the Hoopa Tribe’s Water Quality Control Plan. Concentrations of most nitrogen, phosphorus, and carbon parameters were almost always higher at the Klamath River site than the Trinity River site. Exceedances of the Tribe’s nutrient criteria of 0.035 mg/L total phosphorus (TP) and 0.2 mg/L total nitrogen (TN) were common at the Klamath River site (67% and 60%, respectively) but rare at the Trinity River site (4% and 2%, respectively).

Water Quality, Hoopa Tribal Environmental Protection Agency’s (Hoopa TEPA), Klamath Basin Tribal Water Quality Work Group
2013Crystal Bowman, Grant Johnson, Chook Chook Hillman, Tammy Lightle, Karuk TribeKaruk Tribe Water Quality Assessment Report 2013180102

The Karuk Tribe is the second largest Tribe in California, with over 3,500 Tribal members currently enrolled. The Karuk Tribe is located along the middle Klamath River in northern California. Karuk Ancestral Territory covers over 90 miles of the mainstem Klamath River and numerous tributaries. The Klamath River system is central to the culture of the Karuk People, as it is a vital component of our religion, traditional ceremonies, and subsistence activities. Degraded water quality and quantity has resulted in massive fish kills, increased occurrences of toxic algae, and outbreaks of fish diseases. Impaired water quality conditions also apply extreme limitations and burdens to our cultural activities.

The Karuk Tribe’s Department of Natural Resources has been monitoring daily water quality conditions in the Klamath River since January of 2000 and tributaries to the Klamath River since 1998. The Karuk Tribe has been collaboratively involved in maintaining water quality stations along the Klamath River and its tributaries with the United States Environmental Protection Agency (USEPA), the United States Geological Survey (USGS), the Yurok Tribe, Oregon State University and PacificCorps.

Karuk Tribe, Water Quality, Data Interpretation and Management,
2013Matthew HaningtonFinal 2012 Klamath River Continuous Water Quality Monitoring Summary Report, , 180102

This report summarizes the trends in water quality as measured by Yellow Springs Incorporated (YSI) 6600EDS multi-parameter datasondes on the Klamath and Trinity Rivers from May through November, 2011. The Yurok Tribe Environmental Program (YTEP) measured water quality at several monitoring sites from Weitchpec to the USGS gaging station at Blake’s Riffle at half-hour intervals starting in mid-May and ending in early November. This monitoring was performed in an effort to track both temporal and spatial patterns on the lower reaches of the Klamath River during the sampling period. This data was added to previous years’ water quality data as part of an endeavor to build a multi-year database on the Lower Klamath River. This summary is part of YTEP’s comprehensive program of monitoring and assessment of the chemical, physical, and biological integrity of the Klamath River and its tributaries in a scientific and defensible manner. Datasonde placement along the mainstem of the Klamath and Trinity Rivers and measured parameters were coordinated with the Karuk Tribe and PacifiCorp to expand our understanding of the water quality dynamics in the Klamath basin.

Yurok Tribe Environmental Program (YTEP), Water quality,
2013Matthew Hanington, Kathleen Torso, Yurok Tribe Environmental Program2012 Klamath River Nutrient Summary Report, 180102

This report summarizes the presence and concentration of commonly occurring nutrients and associated analytes on the Klamath and Trinity Rivers during the 2012 sampling season. The Yurok Tribe Environmental Program (YTEP) collected monthly water samples at several monitoring sites from Weitchpec to the Klamath River Estuary in mid-February through mid- April, moved to a bi-weekly interval starting in mid-May and ending in mid-October, followed by monthly sampling in November and December. This sampling was performed in an effort to track both temporal and spatial patterns on the lower reaches of the Klamath and Trinity Rivers during the sampling period. This data was added to previous years’ nutrient data as part of an endeavor to build a multi-year database on the Lower Klamath River. This nutrient summary is part of YTEP’s comprehensive program of monitoring and assessment of the chemical, physical, and biological integrity of the Klamath River and its tributaries in a scientific and defensible manner. Sample events were coordinated with the Karuk and Hoopa Tribes, PacifiCorp, and the Bureau of Reclamation to collect samples during the same day and with comparable methods to expand our understanding of the nutrient dynamics in the Klamath basin.

Klamath River Nutrients, Yurok Tribe Environmental Program (YTEP),
2014Shari K. WitmoreSeasonal growth, retention, and movement of juvenile coho salmon in natural and constructed habitats of mid-Klamath River180102

Juvenile coho salmon (Onchorynchus kisutch) in the Klamath River basin often move long distances when natal streams become inhospitable due to high summer temperatures and high winter flows. Therefore, non-natal rearing sites such as tributaries and off- channel ponds are potentially important to the survival of juvenile coho salmon. This study evaluated the potential benefit to juvenile coho salmon of different types of non-natal rearing habitats in the mid-Klamath watershed including tributaries, beaver-influenced ponds, and constructed off-channel ponds. These sites represent different types of seasonal refugia habitat. Juvenile coho salmon were PIT tagged and measured in ten study sites to evaluate their growth, retention within the habitats, and seasonal movement patterns. Growth rate of fish which reared year-round in the same site was greater in beaver-influenced sites than in other habitat types. Depth, water temperature, volume of habitat, and percent riparian cover were not correlated with growth rates of coho salmon rearing in those sites. However, because I found significant differences in growth rates of fish across individual sites, there may be other habitat characteristics not measured as part of this study that influence growth. Retention rate was positively correlated with average maximum depth; however the summer retention rate of juvenile salmon at the sites was not correlated with salmon growth at the sites. I observed three seasonal movement patterns of juvenile coho salmon: spring redistribution of fry; fall redistribution associated with initial high flows, and outmigration of smolts during the following spring. This exploratory study showed that not only do juvenile coho salmon in the mid-Klamath display several different migratory patterns; choosing different types of off-channel habitats to rear, but the growth and retention rates of those fish depend on complex and site specific characteristics rather than type of habitat.

Coho salmon, natural and constructed habitats, Mid-Klamath river
2014Tamara M. Wood, Heather A. Hendrixson, Douglas F. Markle, Charles S. Erdman, Summer M. Burdick, Craig M. EllsworthSimulation and Validation of Larval Sucker Dispersal and Retention through the Restored Williamson River Delta and Upper Klamath Lake System, Oregon, 18010203

A hydrodynamic model with particle tracking was used to create individual-based simulations to describe larval fish dispersal through the restored Williamson River Delta and into Upper Klamath Lake, Oregon. The model was verified by converting particle ages to larval lengths and comparing these lengths to lengths of larvae in net catches. Correlations of simulated lengths with field data were moderate and suggested a species-specific difference in model performance. Particle trajectories through the delta were affected by wind speed and direction, lake elevation, and shoreline configuration. Once particles entered the lake, transport was a function of current speed and whether behavior enhanced transport (swimming aligned with currents) or countered transport through greater dispersal (faster random swimming). We tested sensitivity to swim speed (higher speeds led to greater dispersal and more retention), shoreline configuration (restoration increased retention relative to pre-restoration conditions), and lake elevation (retention was maximized at an intermediate elevation). The simulations also highlight additional biological questions, such as the extent to which spatially heterogeneous mortality or fish behavior and environmental cues could interact with wind-driven currents and contribute to patterns of dispersal.

Larval Sucker Dispersal, Williamson River Delta, Upper Klamath Lake,
2012Summer M. BurdickDistribution and Condition of Larval and Juvenile Lost River and Shortnose Suckers in the Williamson River Delta Restoration Project and Upper Klamath Lake, Oregon: 2010 Annual Data Summary, 180102

Federally endangered Lost River sucker (Deltistes luxatus) and shortnose sucker (Chasmistes brevirostris) were once abundant throughout their range but populations have declined. They were extirpated from several lakes in the 1920s and may no longer reproduce in other lakes. Poor recruitment to the adult spawning populations is one of several reasons cited for the decline and lack of recovery of these species and may be the consequence of high mortality during juvenile life stages. High larval and juvenile sucker mortality may be exacerbated by an insufficient quantity of suitable or high-quality rearing habitat. In addition, larval suckers may be swept downstream from suitable rearing areas in Upper Klamath Lake into Keno Reservoir, where they are assumed lost to Upper Klamath Lake populations.

This report summarizes data collected in 2010 by the U.S. Geological Survey as a part of this monitoring effort and follows two annual reports on data collected in 2008 and 2009. Restoration modifications made to the Williamson River Delta appeared to provide additional suitable rearing habitat for endangered Lost River and shortnose suckers from 2008 to 2010 based on sucker catches. Mean larval sample density was greater for both species in the Williamson River Delta than adjacent lake habitats in all 3 years. In addition to larval suckers, at least three age classes of juvenile suckers were captured in the delta. The shallow Goose Bay Farms and Tulana Emergent were among the most used habitats by age-0 suckers in 2009. Both of these environments became inaccessible due to low water in 2010, however, and were not sampled after July 19, 2010. In contrast, age-1 sucker catches shifted from the shallow water (about 0.5–1.5 m deep) on the eastern side of the Williamson River Delta in May, to deeper water environments (greater than 2 m) by the end of June or early July in all 3 years.

Lost River sucker (Deltistes luxatus), Shortnose sucker (Chasmistes brevirostris)
2013Barbara A. Martin, David A. Hewitt, Craig M. EllsworthEffects of Chiloquin Dam on Spawning Distribution and Larval Emigration of Lost River, Shortnose, and Klamath Largescale Suckers in the Williamson and Sprague Rivers, Oregon, , , , , 180102

Chiloquin Dam was constructed in 1914 on the Sprague River near the town of Chiloquin, Oregon. The dam was identified as a barrier that potentially inhibited or prevented the upstream spawning migrations and other movements of endangered Lost River (Deltistes luxatus) and shortnose (Chasmistes brevirostris) suckers, as well as other fish species. In 2002, the Bureau of Reclamation led a working group that examined several alternatives to improve fish passage at Chiloquin Dam. Ultimately it was decided that dam removal was the best alternative and the dam was removed in the summer of 2008. The U.S. Geological Survey
conducted a long-term study on the spawning ecology of Lost River, shortnose, and Klamath largescale suckers (Catostomus snyderi) in the Sprague and lower Williamson Rivers from 2004 to 2010. The objective of this study was to evaluate shifts in spawning distribution following the removal of Chiloquin Dam. Radio telemetry was used in conjunction with larval production data and detections of fish tagged with passive integrated transponders (PIT tags) to evaluate whether dam removal resulted in increased utilization of spawning habitat farther upstream in the Sprague River. Increased densities of drifting larvae were observed at a site in the lower Williamson River after the dam was removed, but no substantial changes occurred upstream of the former dam site. Adult spawning migrations primarily were influenced by water temperature and did not change with the removal of the dam. Emigration of larvae consistently occurred about 3–4 weeks after adults migrated into a section of river. Detections of PIT-tagged fish showed increases in the numbers of all three suckers that migrated upstream of the dam site following removal, but the increases for Lost River and shortnose suckers were relatively small compared to the total number of fish that made a spawning migration in a given season. Increases for Klamath largescale suckers were more substantial.

Suckers, Williamson River, Sprague River, Chiloquin Dam
2013Andrew P. Kinziger, Michael Hellmair, David G. Hankin, John Carlos GarzaContemporary Population Structure in Klamath River Basin Chinook Salmon Revealed by Analysis of Microsatellite Genetic Data180102

Chinook Salmon Oncorhynchus tshawytscha exhibit substantial population genetic structure at multiple scales. Although geography is generally more important than life history, particularly migration and run timing, for describing genetic structure in Chinook Salmon, there are several exceptions to this general pattern, and hatchery supplementation has altered natural genetic structure in some areas. Given that genetic structure of Chinook Salmon is often basin-specific, we assessed genetic variation of 27 microsatellite loci in geographically and temporally distinct natural populations and hatchery stocks in the Klamath River basin, California. Multiple analyses support recognition of three major genetic lineages from separate geographic regions in the Klamath River basin: the lower basin, the Klamath River, and the Trinity River. The lower basin group was sharply distinct, but populations in the Klamath and Trinity river lineages were connected by processes that can be described by a one-dimensional, linear, stepping-stone model where gene exchange occurred primarily, but not exclusively, between adjacent populations. Genetic structure by migration timing was also evident, although divergences among populations that differed by migration timing only were fewer than those observed between geographic regions. Distinct run-timing ecotypes in the Klamath River basin thus appear to have evolved independently through a process of parallel evolution. Introgressive pressure from the
hatchery stocks into natural populations was attenuated by distance from the hatchery, but comparison of historical population genetic structure to contemporary patterns would be needed to fully evaluate the extent to which hatchery stocks may have altered natural genetic structure.

Chinook Salmon, Oncorhynchus tshawytscha, Microsatellite Genetic Data, Population Structure
2009ESSA Technologies Ltd. Trinity River Restoration Program: Integrated Assessment Plan Version 1.0 – September 22, 2009180102

The IAP has been under preparation for the last two years and has undergone considerable revision in response to reviews of version 0.90 by the Science Advisory Board (SAB), TMC and TAMWG in 2006, extensive comments from Program partners in 2007, and a final SAB review (www.trrp.net/science/IAP.htm) of IAP version 0.98 in October 2008. Over this time period three workshops attended by SAB members and invited experts were held to refine various components of the IAP. As assessments are conducted and additional information is gained, the IAP must adapt to this improved understanding. Therefore the IAP is intended to be a “living document” that will evolve as we learn more about the Trinity River.

The IAP proposes a sampling framework for conducting the major assessments across subsystems that are required at site, reach and system scales to fulfill the two purposes of the IAP (i.e., feedback to revise management actions; judging progress towards Program goals and subsystem objectives). The sampling framework proposed within the IAP should allow for comparable system-wide estimates generated using alternative approaches (e.g., census or sample). Ongoing assessments with scientifically established protocols will be maintained as long as they provide information at the appropriate scale and the sampling design is statistically sound. The proposed sampling framework allows assessments to fall into one of five different categories: 1) previously established valid protocols (census, sample, and model based); 2) census; 3) General Random Tessellation Stratified (GRTS) panel; 4) alternative sampling design (i.e., assessment requires a unique design); and 5) site-scale design (e.g., process-based study). The intent of this sampling framework is to provide an accepted base structure around which ongoing assessments and future RFPs can be developed and coordinated, and through which data can be combined across disciplines to elucidate cause-effect relations at a system scale.

Adaptive Management, Trinity River, Assessment Needs, Adaptive Environmental Assessment and Management (AEAM), Integrated Assessment Plan (IAP),
2014ESSA Technologies, J. Laurence, Limnotek, Risk Sciences International, Trent University, Trinity Consultants, Dr. John Laurence, Kitimat Modernization Project Sulphur Dioxide Environmental Effects Monitoring Program Program Plan for 2013 to 2018. and Sulphur Dioxide Technical Assessment Report in Support of the 2013 Application to Amend the P2-00001 Multimedia Permit Kitimat Modernization Project Volume 2: Technical Report

This document describes the modeling and monitoring that is planned for the next six years (2013 to 2018) under the sulphur dioxide (SO2) Environmental Effects Monitoring Program for the Kitimat Modernization Project, and thresholds for increased monitoring or mitigation if warranted based on the monitoring results. Rio Tinto Alcan will implement SO2 mitigation strategies if the outcomes of monitoring and modeling described in this plan show adverse impacts causally related to SO2 that are considered to be unacceptable.

The EEM Program is specific to SO2 emissions from KMP. Non-SO2 KMP emissions, emissions and impacts from other facilities, and research and development of new indicators or monitoring methods are all outside of the scope of the EEM Program. The plan distinguishes two types of indicators: key performance indicators (KPIs) which will have quantitative thresholds for increased monitoring or for mitigation, and informative indicators which will provide evidence in support of key performance indicators.

Adaptive Management, Sulphur Dioxide (SO2) Environmental Effects Monitoring Program, Indicators and Thresholds, Atmospheric pathways, Human Health, Mitigation,
2007David R. Marmorek, Marc Porter, Darcy Pickard, Katherine Wieckowski, ESSA Technologies Ltd.Collaborative Systemwide Monitoring and Evaluation Project (CSMEP) Project No. 2003-036-00 Snake River Basin Pilot Report Volume 1 and Volume 2, , , , , ,

The Collaborative Systemwide Monitoring and Evaluation Project (CSMEP) was created for the shared, multi-agency development of a regional monitoring and evaluation (M&E) program for fish populations. It is a bottom-up effort to build consensus to ensure technically and consistently sound programmatic decisions on M&E. Specific goals for CSMEP are to: 1) document, integrate, and make available existing monitoring data on listed salmon, steelhead and other fish species of concern, 2) critically assess strengths and weaknesses of these data for answering high priority monitoring questions, and 3) collaboratively design and help agencies implement improved monitoring and evaluation methods related to key decisions in the Columbia Basin.

Regional M&E for fish populations should be developed through a long-term, systematic process that involves dialogue with Columbia River Basin fish managers and decision makers to identify the key management decisions, spatial and temporal scales of decisions, information needs, time frame for actions, and the level of acceptable risks when making the decisions. It should be recognized that monitoring and evaluation are absolutely critical to the region’s adaptive management cycle.

Decisions on regional M&E designs need to be based on a quantitative evaluation of the costs and benefits of the Status Quo and alternative designs to answer management questions. It will likely be much more cost-effective to build on the strengths of the region’s existing monitoring infrastructure, rather than applying a uniform “cookie-cutter” approach throughout the Columbia River Basin. Each region in the Columbia River Basin has invested considerable resources to develop a monitoring infrastructure that is primarily adapted to address local needs. Improved designs that can overcome weakness in the existing M&E programs should allow assessments at larger spatial and longer temporal scales.

Adaptive Management, Snake River Basin, Habitat, Hatcheries, Integrated Monitoring,
1999David Marmorek, Ian Parnell, Calvin N. Peters, Clint Alexander, ESSA Technologies Ltd.PATH Scoping of Candidate Research, Monitoring and Experimental Management Actions: Concurrently Reducing Key Uncertainties and Recovering Stocks Working Draft, , , , , ,

One of PATH’s original objectives is to assess the ability to distinguish among competing hypotheses from future information, and advise institutions on adaptive management experiments, monitoring, and research that would maximize learning. In the PATH Final Report for Fiscal Year 1998, we set out a plan for addressing this objective (Table ES-1). Following consultation with the Implementation Team (I.T.) early in 1999, PATH established an Experimental Management Workgroup to more clearly define experimental management and generate a list of potential experimental management actions (i.e., the first three tasks in Table ES-1). This report summarizes the progress on these tasks by the experimental management workgroup.

The purpose of this report was to solicit feedback from the I.T., NWPPC, and other regional managers on the PATH experimental management work completed thus far. Specifically, we ask the following questions:
• Are there any actions on the PATH list of candidate actions that are obviously infeasible because of legal/political/practical constraints?
• Are there any actions that should be added to the PATH list of candidate actions?

Clearly there is more work to do, particularly in terms of developing overall strategies, building quantitative assessment tools, and completing the analyses of the relative risks and benefits of alternative experimental actions (i.e., Tasks 4-7 in Table ES-1). However, this report is only the first round of creative exploration of experimental actions. The immediate next step is to narrow the list of potential experimental actions further before proceeding with further quantitative assessments.

PATH, Adaptive management, Lower Columbia River, Lower Snake River,
2016J. Craig Fischenich, Kate E. Buenau, Joseph L. Bonneau, Craig A. Fleming, David R. Marmorek, Marc A. Nelitz, Carol L. Murray, Brian O. Ma, Graham Long, Carl J. Schwarz, US Army Corps of Engineers Engineer Research and Development Center (ERDC), ESSA, Draft Version 6 Science and Adaptive Management Plan Missouri River Recovery Program

The Missouri River Recovery Program (MRRP) is undergoing a transformation resulting from 2011 recommendations by an Independent Science Advisory Panel and the Missouri River Recovery Implementation Committee (MRRIC). An Effects Analysis study established the best available scientific information and provided the foundation for an Adaptive Management Plan (AM Plan) that addresses lingering uncertainties and improves management decisions while implementing actions that avoid jeopardizing the three federally listed species in the system. This draft AM Plan includes a process for resolving critical uncertainties using a framework consisting of four implementation levels: 1) research, 2) in-river testing of hypotheses, 3) scaled implementation of select management actions, and 4) full implementation. The decision criteria for moving to higher levels of implementation are included. A NEPA evaluation of alternative management actions identified an initial suite of actions 12 that will be implemented to meet the objectives of the MRRP. This Draft AM Plan accompanies the Draft Missouri River Recovery Management Plan-Environmental Impact Statement and provides the roadmap for the implementation of the selected alternative and for the identification of subsequent management needs should the initial suite of actions fail to meet objectives. The AM Plan will be implemented collaboratively by the U.S. Army Corps of Engineers, the U.S. Fish and Wildlife Service, and MRRIC following the governance process outlined in the AM Plan.

Missouri River Recovery Program (MRRP), Adaptive Management Plan, Governance, Plovers, Terns, Pallid Sturgeon, Data acquisition, Monitoring, Implementation, Evaluation, Human Considerations
2011Carol Murray, Chad Smith, Dave Marmorek, Dr. David Baasch, Dr. Bridget Barron, Jason Farnsworth, Dr. David Galat, Lorne Greig, Alex Hall, Darcy Pickard, ESSA Technologies Ltd, Headwaters Corporation, University of MissouriMiddle Rio Grande Endangered Species Collaborative Program. Adaptive Management Plan Version 1, ,

The Middle Rio Grande Endangered Species Collaborative Program (Program) is a partnership for the purposes of protecting and improving the status of endangered species in the Middle Rio Grande (MRG) of New Mexico while simultaneously protecting existing and future regional water uses. Two species of particular concern are the Rio Grande silvery minnow (Hybognathus amarus) (silvery minnow) and Southwestern Willow Flycatcher (Empidonax traillii extimus) (flycatcher), both of which are Federally Endangered.

This is Version 1 of the first Adaptive Management (AM) Plan for the Program. It provides a framework for conducting Program activities to deliberately and explicitly reduce management uncertainties. Based on an assessment of the building blocks for AM in Section 1, it identifies a preliminary example AM design in Section 2 and takes this example through the remaining steps in the AM cycle. A more prescriptive Version 2 will take more time to develop, and a process featuring both policy/management and technical roles is recommended for the Program to move to Version 2. It involves a systematic simulation and evaluation of alternative sets of actions, exploring what will best meet the Program‟s goals and concurrently reduce critical management uncertainties under a wide range of possible future conditions. The result would be an accepted and scientifically defensible AM design to be implemented, monitored and evaluated. It also suggests that an AM pilot be considered in the near term, to be done in parallel with the process of developing Version 2.

Middle Rio Grande Endangered Species Collaborative Program, Rio Grande silvery minnow (Hybognathus amarus) (silvery minnow), Southwestern Willow Flycatcher (Empidonax traillii extimus) (flycatcher), Endangered Species
2014Marc Porter, David Marmorek, Darcy Pickard, Katherine Wieckowski, ESSA Technologies Ltd.Dry Creek Adaptive Management Plan (AMP) Final, , , , ,

The Russian River Biological Opinion (RRBIOP, NMFS 2008) identifies the operation of Warm Springs Dam as adversely modifying critical habitat in Dry Creek and jeopardizing coho salmon (endangered) and steelhead (threatened). To alleviate these impacts, the RRBIOP compels the Sonoma County Water Agency (Water Agency) and the United States Army Corps of Engineers (USACE) to implement projects along up to six miles of mainstem Dry Creek. Projects will be designed and implemented with the objective of addressing the lack of low water velocity areas with adequate cover and appropriate water depth that limit habitat suitability for juvenile salmonids in general and juvenile coho salmon in particular. Multiple habitat enhancement projects over the 14 mile length will occur in phases during the 15 year time-period covered by the RRBIOP.

A question raised by the RRBIOP is whether Dry Creek habitat enhancements will have the desired benefits. This question is important both for receiving credit toward the total amount of habitat enhancements set forth in the RRBIOP (six miles) and for assessing the relative effectiveness of various habitat enhancements options. For the latter reason, the RRBIOP states that “an adaptive management, monitoring and evaluation plan” will be developed that identifies “project goals, objectives and success criteria”. ESSA Technologies Ltd. (an independent consulting firm from Vancouver Canada) facilitated the collaborative development of an adaptive management plan (AMP) for Dry Creek in an iterative process of meetings, discussions and document revision. This document captures the outcomes of that process.

The goal of the Dry Creek AMP is to serve as a guide for monitoring juvenile coho and steelhead populations and the habitats they live in over multiple years to detect change resulting from habitat enhancement.

Dry Creek, Adaptive Management, Coho Salmon, Steelhead, Water Quality
2006Clint A.D. Alexander, Calvin N. Peters, David R. Marmorek, Paul HigginsA decision analysis of flow management experiments for Columbia River mountain whitefish (Prosopium williamsoni) management,

High spawning flows from Hugh Keenleyside Dam (HKD) on the Columbia River results in dewatering of eggs in mountain whitefish (Prosopium williamsoni) populations, but the ultimate effect on adult abundance depends on the shape of the egg-to-adult recruitment curve. Our decision analysis assessed the benefits of alternative flow experiments while accounting for uncertainties in this relationship and in flows in the Columbia and Kootenay rivers. The value of experimenting depended on the true recruitment relationship, how we quantified experimental benefits, and experimental design. With current uncertainty, the optimal HKD spawning flow (out of 11 alternative flows) was 1699.2 m3·s–1. Spawning flows below 1699.2 m3·s–1 did not improve egg survival because lower flows rendered highquality spawning habitat unavailable and increased scour mortality. Two experimental designs, both with higher precision monitoring, had a high probability of detecting the true recruitment curve at reasonable cost. Information from these experiments suggested an optimal spawning flow of 1699.2 m3·s–1 if adult abundance were sensitive to egg mortality or 1982.4 m3·s–1 if the population were insensitive.

Columbia River, mountain whitefish, Prosopium williamsoni, British Columbia, Simulated adaptive management,
2012Cynthia ThomsonKlamath Tribes Fishery Socioeconomics Technical Report. For the Secretarial Determination on Whether to Remove Four Dams on the Klamath River in California and Oregon, , , , 180102

In accordance with the terms of the Klamath Hydroelectric Settlement Agreement and contingent on Congressional authorization, the Secretary of the Interior will make a determination regarding whether removal of four Klamath River dams (Iron Gate, Copco 1, Copco 2 and J.C. Boyle) owned by the utility company PacifiCorp advances restoration of salmonid fisheries and is in the public interest. This report analyzes the effects of three alternatives that will be considered by the Secretary as they pertain to fishing opportunities for the Klamath Tribes.

For the Klamath Tribes, the action alternatives are expected to create salmonid harvest opportunities that have been lost for almost a century, allow for eventual subsistence harvest of suckers (which has been lost for 25 years), increase self-sufficiency and self-determination through acquisition of ancestral lands (Mazama Forest), expand engagement in resource monitoring and management, enhance cultural values and practices and their transmission to the next generation, generate jobs and income, and provide greater opportunity for healthy food consumption.

Dam removal, Effects of Alternatives, SONCC, Spring Chinook, Fall Chinook, Steelhead, Pacific Lamprey, Suckers, Redband Trout,
2012Steven A. Stenhouse, Caitlin E. Bean, William R. Chesney, Mark S. PisanoWater Temperature Thresholds for Coho Salmon in a Spring-fed river, Siskiyou County, California, , , , 180102

Coho salmon (Oncorhynchus kisutch) populations in California have declined at an alarming rate in the last 40 to 50 years. Detrimental water temperatures in the Shasta River have contributed to this decline. At one time, the Shasta River was a cool water stream with flows dominated by springs originating from underground flow from Mt. Shasta and snowmelt from the Eddy Mountains. Agricultural practices and water diversions have eliminated much of the historic high-quality aquatic habitat, and only remnants of the once abundant cool water habitat exist. Cool water temperatures are critical for the freshwater phase of the coho salmon life cycle, and are imperative for population recovery. Based on a literature review of the effects of physiology, behavior, and survival of coho salmon, we break water temperatures into optimal, suboptimal, and detrimental ranges. Identifying water temperature thresholds for coho salmon will support the implementation of monitoring stations and adaptive management practices to assure that suboptimal temperature thresholds are not exceeded. It is well documented that the establishment and use of locally determined thresholds as performance criteria in the monitoring and adaptive management of ecosystems is critical to conducting restoration activities. We conclude that protecting the cool water produced by springs located in the upper Shasta River springs complex will improve the likelihood of coho salmon persistence in this watershed and contribute to coho salmon recovery.

California, cold water springs, Coho Salmon, Oncorhychus Kisutch, Rearing habitat, Recovery, Temperature, Thresholds, Shasta River, Siskiyou County
2017Roger J. Peters, Martin Liermann, Michael L. McHenry, Paul Bakke, George R. PessChanges in Streambed Composition in Salmonid Spawning Habitat of the Elwha River during Dam Removal, , ,

One uncertainty associated with large dam removal is the level of downstream sediment deposition and associated short-term biological effects, particularly on salmonid spawning habitat. Recent studies report downstream sediment deposition following dam removal is influenced by proximity to the source and river transport capacity. The impacts of dam removal sediment releases are difficult to generalize due to the relatively small number of dam removals completed, the variation in release strategies, and the physical nature of systems. Changes to sediment deposition and associated streambed composition in the Elwha River, Washington State, were monitored prior to (2010-2011) and during (2012-2014) the simultaneous removal of two large dams (32 and 64 m). Changes in the surface layer substrate composition during dam removal varied by year and channel type. Riffles in floodplain channels downstream of the dams fined and remained sand dominated throughout the study period, and exceeded levels known to be detrimental to incubating salmonids. Mainstem riffles tended to fine to gravel, but appear to be trending toward cobble after the majority of the sediment was released and transported through system. Thus, salmonid spawning habitats in the mainstem appear to have been minimally impacted while those in floodplain channels appear to have been severely impacted during dam removal.

sediment, sediment transport, sediment composition, restoration, environmental impacts
1997Russell F. Thurow , Danny C. Lee, Bruce E. RiemanDistribution and Status of Seven Native Salmonids in the Interior Columbia River Basin and Portions of the Klamath River and Great Basins180102

We summarized presence, absence, current status, and potential historical distribution of seven native salmonid taxa—bull trout Salvelinus conjluentus, Yellowstone cutthroat trout Oncorhyncus clarki bouvieri. westslope cutthroat trout O. c. lewisi, redband trout and steelhead ,stream type (age-1 migrant) chinook salmon and ocean type (age-0 migrant) chinook salmon—in the interior Columbia River basin and portions of the Klamath River and Great basins. Potential historical range was defined as the likely distribution in the study area prior to European settlement. Data were compiled from existing sources and surveys completed by more than 150 biologists. Within the potential range of polamodromous salmonids, status was unknown in 38-69% of the area, and the distribution of anadromous salmonids was unknown in 12-l5%. We developed models to quantitatively explore relationships among fish status and distribution, the biophysical environment, and land management, and used the models to predict the presence of taxa in unsampled areas. The composition, distribution, and status of fishes within the study area is very different than it was historically. Although several of the salmonid taxa are distributed throughout most of their potential range, declines in abundance and distribution and fragmentation into smaller patches are apparent for all forms. None of the salmonid taxa have known or predicted strong populations in more than 22% of their potential ranges, with the exception of Yellowstone cutthroat trout. Both forms of chinook salmon are absent from more than 70% and steelhead from more than 50% of their potential ranges, and all are approaching extirpation in portions of their remaining ranges.

Bull Trout, Salvelinus confluentus,
2009E. A. Mora, S. T. Lindley, D. L. Erickson, A. P. KlimleyDo impassable dams and flow regulation constrain the distribution of green sturgeon in the Sacramento River, California?, ,

Conservation of the threatened green sturgeon Acipenser medirostris in the Sacramento River of California is impeded by lack of information on its historical distribution and an understanding of how impassable dams and altered hydrographs are influencing its distribution. The habitat preferences of green sturgeon are characterized in terms of river discharge, velocity, channel gradient, and air temperature associated with
2590 sightings of green sturgeon in the Klamath and Rogue rivers using the Mahalanobis distance D2, a multivariate measure of distance from the mean habitat conditions associated with the sightings. D2 was then calculated for reaches of the Sacramento and San Joaquin rivers and their tributaries under historic and current (2007) hydrographs to assess where and when habitat conditions in the Sacramento–San Joaquin basin are similar to those known to support green sturgeon. The model for current habitat conditions was validated with observations of acoustically-tagged green sturgeon at large in the basin in 2007. The model predicts that in the absence of impassable dams and altered hydrographs, green sturgeon would utilize the mainstem Sacramento and San Joaquin rivers, and several major tributaries including portions of the lower Feather River, American River, and Yuba River. While dams block access to about 9% of historically available habitat, it is likely that the blocked areas contained relatively high amounts of spawning habitat because of their upstream position in the river network. Flow regulation below the reservoirs has mixed effects on habitat suitability for green sturgeon, with many reaches showing increased suitability in winter and spring, but with some reaches showing decreased suitability in many months, particularly late spring through early autumn.

Green sturgeon, Acipenser medirostris, Conservation,
2011Timothy D. Mayer, Seth W. NamanStreamflow response to Climate as Influenced by Geology and Elevation, 180102

This study examines the regional streamflow response in 25 predominately unregulated basins to warmer winter temperatures and snowpack reductions over the last half century in the Klamath Basin of California and Oregon. Geologic controls of streamflow in the region result in two general stream types: surfacedominated and groundwater-dominated basins. Surface-dominated basins were further differentiated into rain basins and snowmelt basins on the basis of elevation and timing of winter runoff. Streamflow characteristics and response to climate vary with stream type, as discussed in the study. Warmer winter temperatures and snowpack reductions have caused significantly earlier runoff peaks in both snowmelt and groundwater basins in the region. In the groundwater basins, the streamflow response to changes in snowpack is smoothed and delayed and the effects are extended longer in the summer. Our results indicate that absolute decreases in July-September base flows are significantly greater, by an order of magnitude, in groundwater basins compared to surface dominated basins. The declines are important because groundwater basins sustain Upper Klamath Lake inflows and mainstem river flows during the typically dry summers of the area. Upper Klamath Lake April September net inflows have decreased an estimated 16% or 84 thousand acre-feet (103.6 Mm3) since 1961, with the summer months showing proportionately more decline. These changes will exacerbate water supply problems for agriculture and natural resources in the region.

Climate Change ⁄ variability, Klamath Basin, Groundwater hydrology, Surface water / Groundwater interactions, Base-flow index, Upper Klamath Lake
2015Klimley, A. Peter, Chapman, Eric D., Cech, Jr., Joseph J., Cocherell, Dennis E., Fangue, Nann A., Gingras, Marty, Jackson, Zachary, Miller, Emily A., Mora, Ethan A., Poletto, Jamilynn B., Schreier, Andrea M., Seesholtz, Alicia, Sulak, Kenneth J., Thomas, Michael J., U Woodbury, David, Wyman, Megan T.,Sturgeon in the Sacramento–San Joaquin Watershed: New Insights to Support Conservation and Management

The goal of a day-long symposium on March 3, 2015, Sturgeon in the Sacramento–San Joaquin Watershed: New Insights to Support Conservation and Management, was to present new information about the physiology, behavior, and ecology of the green (Acipenser medirostris) and white sturgeon (Acipenser transmontanus) to help guide enhanced management and conservation efforts within the Sacramento–San Joaquin watershed. This symposium identified current unknowns and highlighted new electronic tracking technologies and physiological techniques to address these knowledge gaps. A number of presentations, each reviewing ongoing research on the two species, was followed by a round-table discussion, in which each of the participants was asked to share recom-mendations for future research on sturgeon in the watershed. This article presents an in-depth review of the scientific information presented at the symposium with a summary of recommendations for future research.

Green sturgeon, Acipenser medirostris, White sturgeon, Acipenser transmontanus, Conservation biology
2012David A. Hewitt, Eric C. Janney, Brian S. Hayes, Alta C. HarrisDemographics and Run Timing of Adult Lost River (Deltistes luxatus) and Shortnose (Chasmistes brevirostris) Suckers in Upper Klamath Lake, Oregon, 2011, 18010206

Data from a long-term capture-recapture program were used to assess the status and dynamics of populations of two long-lived, federally endangered catostomids in Upper Klamath Lake, Oregon. Lost River suckers (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris) have been captured and tagged with passive integrated transponder (PIT) tags during their spawning migrations in each year since 1995. In addition, beginning in 2005, individuals that had been previously PIT-tagged were re-encountered on remote underwater antennas deployed throughout sucker spawning areas. Captures and remote encounters during spring 2011 were used to describe the spawning migrations in that year and also were incorporated into capture-recapture analyses of population dynamics.

Despite relatively high survival in most years, both species have experienced substantial declines in the abundance of spawning fish because losses from mortality have not been balanced by recruitment of new individuals. Although capture-recapture data indicate substantial recruitment of new individuals into the adult spawning populations for SNS and river spawning LRS in some years, size data do not corroborate these estimates. In fact, fork length data indicate that all populations are largely comprised of fish that were present in the late 1990s and early 2000s. As a result, the status of the endangered sucker populations in Upper Klamath Lake remains worrisome, and the situation is most dire for shortnose suckers. Future investigations should explore the connections between sucker recruitment and survival and various environmental factors, such as water quality and disease. Our monitoring program provides a robust platform for estimating vital population parameters, evaluating the status of the populations, and assessing the effectiveness of conservation and recovery efforts.

Lost River suckers, Deltistes luxatus, Shortnose suckers, Chasmistes brevirostris
2006Gathard Engineering ConsultingKlamath River Dam and Sediment Investigation, , 180102

The State Coastal Conservancy (Conservancy) and the Ocean Protection Council (OPC), two agencies of the State of California, initiated this study to characterize sediment behind four dams of the Klamath River Hydroelectric Project on the Klamath River, and examine the possibility of dam removal. This study investigates removal of the four most downstream dams: Iron Gate, Copco 2, Copco 1 and J.C. Boyle.

The Klamath River is located in northern California and southern Oregon on the Pacific coast of the United States. The Klamath River Hydroelectric Project, owned by PacifiCorp, consists of six generating developments along the mainstem of the Upper Klamath River. The project also includes a re-regulation dam with no generation facilities, and one generating development on Fall Creek, a tributary to the Klamath River. The Klamath River Project is now undergoing relicensing proceedings before the Federal Energy Regulatory Commission (FERC). Separate from the formal FERC relicensing process, a Settlement Group has explored future project management alternatives, and its Dam Removal Subgroup has investigated dam removal as a project management alternative.

Previous dam removal studies have suggested that downstream erosion of sediment to the marine environment would be a feasible approach to dam removal and sediment management, but this conclusion was limited by the lack of information characterizing sediment quantity, quality, and management options. Therefore, the Subgroup asked the Conservancy to conduct a detailed reservoir sediment study and dam removal investigation. The Conservancy entered into contracts with Gathard Engineering Consulting (GEC) and Shannon and Wilson, Inc., (S&W) to characterize sediment located behind the four lowermost dams, and to conduct preliminary dam removal studies.

Sediment,
1983P. Futer, M. NassichukMetals in Eulachons from the Nass River and Crabs from Alice Arm, B.C.,

In 1981, Amax Molybdenum of Canada Ltd. began discharging tailings from its molybdenum mine at Kitsault, British Columbia into Alice Arm. Native Indians living in coastal areas of Northern B.C. expressed concern with respect to the potential for metal contamination of certain food f ish and invertebrates as a result of the tailings disposal. In response to this concern, the Department of Fisheries and Oceans carried out a sampling program in 1981 and 1982 to determine the metal content of Nass River eulachons (Thaleichthys pacificus) and small numbers of King crab (Paralithodes camtschatica) and Tanner crab (Chionoecetes bairdl) from Alice Arm. Levels of arsenic, cadmium, chromium, copper, manganese, mercury, molybdenum, nickel, lead and zinc were measured in organisms sampled. This report presents results of the sampling program and compares them with metal data from organisms previously collected from coastal waters of British Columbia and other selected coastal locations throughout the world.

Eulachons, Metals
2009Charles S. Erdman, Heather A. HendrixsonLarval Shortnose and Lost River Sucker Response to Large Scale Wetland Restoration of the North Half of the Williamson River Delta Preserve, Oregon, 18010201

Hydrologic reconnection of deltaic wetlands at the mouth of the Williamson River with portions of Agency Lake and Upper Klamath Lake, Oregon is a restoration strategy aimed at increasing the amount of nursery habitat available for larval Lost River suckers Deltistes luxatus and shortnose suckers Chasmistes brevirostris. We examined the response of larval suckers to this large scale wetland restoration project at the Williamson River Delta by assessing discrepancies in catch rates, habitat preferences, and fish condition (size and gut fullness) at restored and existing lakeshore fringe wetlands. Differences in habitat associations existed between the two wetland types, as larval suckers preferred shallow, vegetated areas in the restored areas of the Williamson River Delta while in existing wetlands deep, non vegetated areas were occupied more frequently. Mean larval sucker length and gut fullness in the restored areas were on average greater than means in existing wetlands, a strong indication that larvae were rearing in the restored wetlands of the Williamson River Delta. Our monitoring suggests that wetland restoration efforts at the Williamson River Delta may contribute to the recovery of these two endangered species through the increase of larval nursery habitat.

Lost River suckers, Deltistes luxatus, Shortnose suckers, Chasmistes brevirostris
1998Robert M. Durborow, Andrew J. Mitchell, M. David CrosbyIch (White Spot Disease),

Ich is a common name for the parasite Ichthyophthirius multifiliis and the disease that it causes. The parasite is capable of killing large numbers of fish in a short period of time. Early diagnosis and treatment are essential for controlling Ich and reducing fish losses. Prevention of this disease is, of course, the best method of avoiding fish mortalities.

Ich, Ichthyophthirius multifiliis, Prevention, Treatment,
2000Michael Cooperman, Douglas F. MarkleEcology of Upper Klamath Lake Shortnose and Lost River Suckers 2. Larval Ecology of Shortnose and Lost River suckers in the lower Williamson River and Upper Klamath Lake18010206

The larval life history stage of Klamath Basin suckers has received relatively little study. However, the early life history stages of endangered shortnose and Lost River suckers are targets for much of the restoration activity in the basin, including the restoration of the lower Williamson River delta at Tulana Farms.

This study is part of doctoral dissertation work begun in 1998. Primary questions being evaluated are: I ) whether significant early life history events take place in the Williamson River; 2) whether habitat selection changes with age or location; 3) whether feeding habits change with age or location; 4) whether community structure influences larval sucker survival; and 5) whether differences exist between Lost River and shortnose sucker early life histories. Sampling in 1998 was partly exploratory and was used to guide subsequent sampling in 1999. This report is based on the 1998 sampling but includes preliminary comments on aspects of the 1999 data.

Lake Shortnose Suckers, Lost River Suckers, Larval Ecology
2007Kurtis BrownEvidence of spawning by green sturgeon, Acipenser medirostris, in the upper Sacramento River, California

This study reports the only direct evidence of spawning of green sturgeon, Acipenser medirostris, in the upper Sacramento River, CA. Two green sturgeon eggs were collected with substrate mats immediately below Red Bluff Diversion Dam. One green sturgeon larva was collected with a larval net at Bend Bridge. We concluded that green sturgeon spawn in the upper Sacramento River, both above and below RBDD. Temperature ranges in the study area (10–15C) are similar to conditions used in successful artificial rearing of green sturgeon and do not appear to be a limiting factor to successful spawning of green sturgeon; however, suitable habitat upstream of RBDD is inaccessible when dam gates are lowered.

Green Sturgeon, Acipenser medirostris, Artificial substrates, Larval nets, Rotary-screw traps, Migration, Red Bluff Diversion Dam
2010Mark R. Terwilliger, Tamal Reece, Douglas F. MarkleHistoric and recent age structure and growth of endangered Lost River and shortnose suckers in Upper Klamath Lake, Oregon, 18010206

Seventy-four lapilli from Lost River suckers captured in Upper Klamath Lake in 1970 during a snag fishery on spawning adults and 192 lapilli from adults sacrificed from 2001–2006 were examined to
determine age and growth parameters; lapilli from 165 shortnose suckers sacrificed from Upper Klamath Lake from 2001–2006 were also examined. Relative marginal distance analyses indicated that growth marks were annuli and formed in December–January. Lost River suckers from the historic collection were aged to 57 years, while Lost River and shortnose suckers from the recent collection were aged to 40 years and 24 years, respectively. Larger and older Lost River suckers were represented in the historic collection compared to the recent collection. Uncoupling of otolith length and fish length in Lost River suckers as well as a large spread in the predicted age- at-size for shortnose suckers precluded the ability to back-calculate size-at-age. Likelihood ratio tests indicated the growth model parameters were
significantly different at both the sex and collection level. Growth in body length for both species appeared determinate in that growth was rapid until maturity, and then slowed over several years until growth in length was nearly nonexistent; a 650– 700 mm Lost River sucker could be between 14 and 57 years old, while a 460 mm shortnose sucker could range from 12–24 years old. In contrast, while growth in body length slowed for both species, body mass continued to increase. This growth strategy, which is also found in other western lake suckers, may allow for more energy to be utilized for reproduction and help populations persist in spite of years of limited recruitment or recruitment failure.

Age, Growth, Upper Klamath Lake, Lost River Sucker, Shortnose sucker
2015David A. Hewitt, Eric C. Janney, Brian S. Hayes, Alta C. HarrisStatus and Trends of Adult Lost River (Deltistes luxatus) and Shortnose (Chasmistes brevirostris) Sucker Populations in Upper Klamath Lake, Oregon, 201418010206

Data from a long-term capture-recapture program were used to assess the status and dynamics of populations of two long-lived, federally endangered catostomids in Upper Klamath Lake, Oregon. Lost River suckers (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris) have been captured and tagged with passive integrated transponder (PIT) tags during their spawning migrations in each year since 1995. In addition, beginning in 2005, individuals that had been previously PIT-tagged were re-encountered on remote underwater antennas deployed throughout sucker spawning areas. Captures and remote encounters during the spawning season in spring 2014 were incorporated into capture-recapture analyses of population dynamics.

Cormack-Jolly-Seber (CJS) open population capture-recapture models were used to estimate annual survival probabilities, and a reverse-time analog of the CJS model was used to estimate recruitment of new individuals into the spawning populations. In addition, data on the size composition of captured fish were examined to provide corroborating evidence of recruitment. Model estimates of survival and recruitment were used to derive estimates of changes in population size over time and to determine the status of the populations through 2013. Separate analyses were conducted for each species and also for each subpopulation of Lost River suckers (LRS). Shortnose suckers (SNS) and one subpopulation of LRS migrate into tributary rivers to spawn, whereas the other LRS subpopulation spawns at groundwater upwelling areas along the eastern shoreline of the lake.

Lost River Sucker, Deltistes luxatus, Shortnose Sucker, Chasmistes brevirostris, Population Status and Trends
2016Danielle M. Hereford, Carl O. Ostberg, Summer M. BurdickPredation on Larval Suckers in the Williamson River Delta Revealed by Molecular Genetic Assays—A Pilot Study18010201

Predation of endangered Lost River suckers (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris) during larval egress to Upper Klamath Lake from the Williamson River is poorly understood but may be an important factor limiting recruitment into adult spawning populations. Native and non-native piscivores are abundant in nursery wetland habitat, but larval predation has not been directly studied for all species. Larvae lack hard body structures and digest rapidly in predator digestive systems. Therefore, traditional visual methods for diet analysis may fail to identify the extent of predation on larvae. The goals of this study were to (1) use quantitative polymerase chain reaction (qPCR) and single nucleotide polymorphism (SNP) assays developed for Lost River and shortnose suckers to assay predator stomach contents for sucker DNA, and (2) to assess our ability to use this technique to study predation. Predators were captured opportunistically during larval sucker egress. Concurrent feeding trials indicate that most predators—yellow perch (Perca flaverscens), fathead minnow (Pimephales promelas), blue chub (Gila coerulea), Klamath tui chub (Siphatales bicolor bicolor), Klamath Lake sculpin (Cottus princeps), slender sculpin (Cottus tenuis)—preyed on sucker larvae in the laboratory. However, sucker DNA was not detected in fathead minnow stomachs. Of the stomachs screened from fish captured in the Williamson River Delta, 15.6 percent of yellow perch contained sucker DNA. This study has demonstrated that the application of qPCR and SNP assays is effective for studying predation on larval suckers. We suggest that techniques associated with dissection or detection of sucker DNA from fathead minnow stomachs need improvement.

Predation, Larval Suckers,
2016Julie Day, Ron Barnes, Kirk Groves, Darrick Weissenfluh,Klamath Falls Sucker Assisted Rearing Program 2016 Update18010206

The goal of U.S Fish and Wildlife Service’s (USFWS) Sucker Assist Rearing Program (SARP) is to rear 8,000-10,000 age-0 Lost River and shortnose suckers to >200 mm for reintroduction into the Upper Klamath Lake (UKL) system. USFWS employees, with help from Bureau of Reclamation (Reclamation) and The Klamath Tribes (TKT), successfully collected an estimated 4,300 larvae from the Williamson River in 2016 and transported them to Gone Fishing. SARP had an estimated 70% survival rate from collection to ponding. Expansion in 2016 will double the current rearing capacity and allow SARP to rear the target number of suckers in low densities as well as investigate experimental salvage fish health treatment efficacy and more specific rearing questions. It will also allow us to hold fish in discrete cohorts throughout their captivity in an effort to differentiate spawning yields among the UKL sucker species.

Sucker Assist Rearing Program, SARP
2016Summer M. Burdick, Carl O. Ostberg, Mark E. Hereford, Marshal S. HoyJuvenile Sucker Cohort Tracking Data Summary and Assessment of Monitoring Program, 201518010206

Populations of federally endangered Lost River (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris) in Upper Klamath Lake, Oregon, are experiencing long-term declines in abundance. Upper Klamath Lake populations are decreasing because adult mortality, which is relatively low, is not being balanced by recruitment of young adult suckers into known adult spawning aggregations. Previous sampling for juvenile suckers indicated that most juvenile sucker mortality in Upper Klamath Lake likely occurs within the first year of life. The importance of juvenile sucker mortality to the dynamics of Clear Lake Reservoir populations is less clear, and factors other than juvenile mortality (such as access to spawning habitat) play a substantial role. For example, production of age-0 juvenile suckers, as determined by fin ray annuli and fin development, has not been detected since 2013 in Clear Lake Reservoir, whereas it is detected annually in Upper Klamath Lake.

We initiated a long-term juvenile sucker monitoring program in 2015 designed to track cohorts through seasons and among years in both Upper Klamath Lake and Clear Lake Reservoir. Specifically, our goals are to track annual variability in age-0 sucker production, juvenile sucker survival, growth, and condition. In this first year of the monitoring program, we assessed assumptions that sampled fish were representative of populations of suckers in each lake. The size, age, and species composition of suckers were similar between randomly determined sites and fixed sites in each lake. We captured a wide size and age range of suckers using similar gear, indicating our gear did not exclude older and larger fish. We identified improvements that could be made in the monitoring program including increasing the number of randomly determined sample sites in both lakes, evaluation of gear-size selectivity, and validation of aging methods for juvenile Lost River and shortnose suckers.

Lost River Sucker, Deltistes luxatus, Shortnose sucker, Chasmistes brevirostris,
2015Summer M. Burdick, Diane G. Elliott, Carl O. Ostberg, Carla M. Conway, Amari Dolan-Caret, Marshal S. Hoy, Kevin P. Feltz, Kathy R. EcholsHealth and Condition of Endangered Juvenile Lost River and Shortnose Suckers Relative to Water Quality and Fish Assemblages in Upper Klamath Lake, Oregon, and Clear Lake Reservoir, California, 18010206

Most mortality of endangered Lost River (Deltistes luxatus) and shortnose (Chasmistes brevirostris) suckers in Upper Klamath Lake, Oregon, appears to occur within the first year of life. However, juvenile suckers in Clear Lake Reservoir, California, appear to survive longer and may even recruit to the spawning populations. Our goal in this study was to develop productive lines of inquiry into the causes of mortality of juvenile suckers, especially in Upper Klamath Lake, through comparison of sucker health and environmental conditions in both lakes. The health of juvenile suckers was associated with physical, biological, and chemical characteristics in each lake from July to September 2013 and 2014.

Differences in sucker health and condition between lakes were considered the most promising clues to the causes of differential juvenile sucker morality between lakes. A low prevalence of petechial hemorrhaging of the skin (16 percent) and deformed opercula (8 percent) in Upper Klamath Lake suckers may indicate exposure to a toxin other than microcystin. Suckers grew slower in their first year of life, but had similar or greater triglyceride and glycogen levels in Upper Klamath Lake compared to Clear Lake Reservoir. These findings do not suggest a lack of prey quantity but may indicate lower prey quality in Upper Klamath Lake.

Lost River Sucker, Deltistes luxatus, Shortnose suckers, Chasmistes brevirostris,
2015Summer M. Burdick, David A. Hewitt, Josh E. Rasmussen, Brian S. Hayes, Eric C. Janney, Alta C. HarrisEffects of Lake Surface Elevation on Shoreline- Spawning Lost River Suckers, , , 18010206

We analyzed remote detection data from PIT-tagged Lost River Suckers Deltistes luxatus at four shoreline spawning areas in Upper Klamath Lake, Oregon, to determine whether spawning of this endangered species was affected by low water levels. Our investigation was motivated by the observation that the surface elevation of the lake during the 2010 spawning season was the lowest in 38 years. Irrigation withdrawals in 2009 that were not replenished by subsequent winter–spring inflows caused a reduction in available shoreline spawning habitat in 2010. We compared metrics of skipped spawning, movement among spawning areas, and spawning duration across 8 years (2006–2013) that had contrasting spring water levels. Some aspects of sucker spawning were similar in all years, including few individuals straying from the shoreline areas to spawning locations in lake tributaries and consistent effects of increasing water temperatures on the accumulation of fish at the spawning areas. During the extreme low water year of 2010, 14% fewer female and 8% fewer male suckers joined the shoreline spawning aggregation than in the other years. Both males and females visited fewer spawning areas within Upper Klamath Lake in 2010 than in other years, and the median duration at spawning areas in 2010 was at least 36% shorter for females and 20% shorter for males relative to other years. Given the imperiled status of the species and the declining abundance of the population in Upper Klamath Lake, any reduction in spawning success and egg production could negatively impact recovery efforts. Our results indicate that lake surface elevations above 1,262.3–1,262.5 m would be unlikely to limit the number of spawning fish and overall egg production.

PIT tagging, Lost River Suckers, Deltistes luxatus
2009Nolan P. Banish, Barbara J. Adams, Rip S. Shively, Michael M. Mazur, David A. Beauchamp, Tamara M. WoodDistribution and Habitat Associations of Radio-Tagged Adult Lost River Suckers and Shortnose Suckers in Upper Klamath Lake, Oregon18010206

Radiotelemetry was used to investigate the summer distribution and diel habitat associations of endangered adult Lost River suckers Deltistes luxatus and shortnose suckers Chasmistes brevirostris in northern Upper Klamath Lake, Oregon. From 2002 to 2004, Lost River and shortnose suckers were tracked by boat, and water depth and water quality were measured at each fish location. A series of water quality monitors were deployed in northern Upper Klamath Lake to provide temporal information on ambient temperature, pH, and dissolved oxygen, and water samples were collected to assess chlorophyll a concentration. Suckers moved into northern Upper Klamath Lake during June and began to leave in late September each year. Kernel density estimates revealed differences in the distribution in the northern portion of Upper Klamath Lake in 2002 and 2004. In 2003, however, both Lost River and shortnose suckers were commonly located within and offshore from Pelican Bay, a shallow (1.0–2.0 m), groundwater-influenced area of Upper Klamath Lake. This was especially obvious beginning in late July of 2003, concurrent with reduced dissolved oxygen levels (,4.0 mg/L) in the northern portion of Upper Klamath Lake that resulted from a dieoff of the cyanobacterium Aphanizomenon flos-aquae. Both Lost River and shortnose suckers were generally associated with water depths greater than the mean depth (2.8 m) of northern Upper Klamath Lake. Evidence
ratios did not suggest diel differences in depth, temperature, dissolved oxygen, or pH at sucker locations. Both Lost River and shortnose suckers generally occupied depths greater than 2.0 m, except when suckers sought refuge in Pelican Bay during periods of poor water quality. Despite the potential for increased avian predation, suckers appeared to benefit from moving into Pelican Bay rather than staying in areas where dissolved oxygen was low. Pelican Bay appears to be an important refugium and thus may be important for sucker conservation.

Lost River suckers, Deltistes luxatus, Shortnose suckers, Chasmistes brevirostris, Upper Klamath Lake, Distribution
2006Joel P. Van Eenennaam , Javier Linares , Serge I. Doroshov , David C. Hillemeier , Thomas E. Willson, Arnold A. NovaReproductive Conditions of the Klamath River Green Sturgeon180102

Reproductive characteristics of the adult Klamath River green sturgeon Acipenser medirostris were studied during the spawning migration. The locations of captures were from the mouth of the Klamath River upstream to river kilometer 72. A total of 82 females and 118 males were sampled for age, sex, body size, gonad weight, fecundity, egg size, and gonadal histology during April–July for five consecutive years (1999–2003). All fish sampled were considered mature adults, except for two immature males (body weight, 10 and 16 kg) captured close to the mouth of the river. The average body weight for males and females was 32 and 46 kg, respectively. The condition factor ranged from 0.60 to 0.92 for males and from 0.65 to 0.94 for females. The long tapered body conformation for both sexes made it difficult to sex individuals by external morphology, but in general, the females had a slightly more robust conformation. The fork length range was 139–199 cm in males and 151–223 cm in females. The majority (.90%) of males were 15–28 years old, and females were 19–34 years old. In all females the preovulatory condition was distinguished by the migration of the germinal vesicle to the animal pole, and the mean polarization index (distance of the germinal vesicle from the animal pole divided by oocyte diameter) was 0.042. The gonadosomatic index for females ranged from 7% to 17% and that for males from 2% to 8%. Individual and relative fecundity ranges were 59,000–242,000 and 2,000–4,000 eggs, respectively. The fully grown eggs were the largest recorded for North American sturgeon, averaging 4.33 mm in diameter. Although this study indicates that the Klamath River supports an important and potentially stable spawning migration, continued monitoring of the population and identification of spawning and nursery sites are critical for the long-term preservation of this species.

Green Sturgeon, Reproductive Conditions
2016M. L. Moser, J. A. Israel, M. Neuman, S. T. Lindley, D. L. Erickson, B. W. McCovey Jr, A. P. KlimleyBiology and life history of Green Sturgeon (Acipenser medirostris Ayres, 1854): state of the science

Green Sturgeon (GRS) Acipenser medirostris is one of the most marine-oriented of all sturgeons. It primarily spawns in the Sacramento, Klamath, and Rogue Rivers, yet lives most of its life in estuarine and coastal waters along the West Coast of North America. Spawning is only known to occur in the Rogue, Klamath and Sacramento rivers and optimal temperatures for egg incubation and larval growth are not always maintained in these dammed and highly regulated systems. Genetic analysis and acoustic telemetry have confirmed the presence of two genetically distinct populations; the southern population is listed as “threatened” under the ESA. Adults only enter natal rivers to spawn every 1–4 years. They make extensive coastal migrations in depths <80 m and move between estuaries where they aggregate in summer. The long marine occupancy of GRS potentially exposes them to mortality from various marine activities such as bottom trawl fishing, dredging, and ocean energy projects, but also provides a theoretical reservoir of fish to support viable populations. Critically-needed information for protection of this species includes: accurate annual population size estimates, data on distribution and habitat requirements for larvae and juveniles, and assessment of mortality due to bycatch, poaching and marine mammal predation.

Green Sturgeon, Distribution, Abundance,
2014Phaedra Doukakis,2014 Informal status review for the Northern Distinct Population Segment of the North American green sturgeon (Acipenser medirostris)

This review examines new information about the Northern Distinct Population Segment (DPS) of green sturgeon (Acipenser medirostris) to assess its status as a Species of Concern (i.e., to verify whether its current position on the NMFS Species of Concern List is still appropriate). Based on the last status review in 2005, NMFS concluded that the Northern DPS did not warrant listing under the Endangered Species Act (ESA), but designated the species as a NMFS Species of Concern, due to concerns about fisheries harvest, alterations to freshwater habitat, and the lack of population data. The following summarizes our evaluation of and conclusions based on the new information that has become available since 2005 about the Northern DPS’ abundance, productivity, distribution, life history characteristics, and threats.

Endangered Species Act (ESA), North American green sturgeon (Acipenser medirostris),
2007Ryan L. Benson, Scott Turo, Barry W. McCovey Jr.Migration and movement patterns of green sturgeon (Acipenser medirostris) in the Klamath and Trinity rivers, California, USA18010209

Green sturgeon, Acipenser medirostris, movement and migration within the Klamath and Trinity rivers were assessed using radio and sonic telemetry. Sexually mature green sturgeon were captured with gillnets in the spring, as adults migrated upstream to spawn. In total, 49 green sturgeon were tagged with radio and/or sonic telemetry tags and tracked manually or with receiver arrays from 2002 to 2004. Tagged individuals exhibited four movement patterns: upstream spawning migration, spring outmigration to the ocean, or summer holding, and outmigration after summer holding. Spawning migrations occurred from April to June, as adultsmoved fromthe ocean upstreamto spawning sites. Approximately 18%of adults, those not out mignation in the spring, made spring postspawning outmigrations. The majority of adults, those not outmigrating in the spring, remained in discrete locations characterized as deep, low velocity pools for extended periods during the summer and early fall. Fall outmigration occurred when fish left summer holding locations, traveled rapidly downstream, and exited the river system.High river discharge due to the onset of winter rainstorms and freshets appear to be the key environmental cue instigating the fall outmigration.

Acipenseridae, Sonic telemetry, Radio telemetry, Summer holding, Outmigration, River discharge
2002Peter B. Adams, Churchill B. Grimes, Joseph E. Hightower, Steven T. Lindley, Mary L. MoserStatus Review for North American Green Sturgeon, Acipenser medirostris

In 2001, the National Marine Fisheries Service (NMFS) received a petition requesting Endangered Species Act (ESA) listing of North American green sturgeon (Acipenser medirostris) as a threatened or endangered species. In response to this petition, NMFS announced that it would initiate an ESA status review. The ESA allows the listing of A Distinct Population Segments@ (DPSs) of vertebrates as well as named species and subspecies. The combined U. S. Fish and Wildlife Service and NMFS policy on recognition of DPSs outlines two tests to identify separate units: discreteness and significance. A DPS may be considered discrete if it is markedly separate from other populations of the same taxon as a consequence of physical, physiological, ecological, or behavioral factors or if it is delimited by international governmental boundaries. The significance of the population will be decided on the basis of considerations including, but not limited to its persistence, evidence that loss of the DPS would result in a significant gap in spatial structure, evidence of the DPS representing the only surviving natural occurrence of a taxon, or evidence that the DPS differs markedly in its genetic characteristics. Once a DPS has been identified, a risk assessment is preformed to determine whether a listing is warranted for that unit.

Green sturgeon have a complex anadromous life history. They spend more time in the ocean than any other sturgeon. The majority of green sturgeon are thought to spawn in the Klamath River, but spawning also occurs in the Sacramento and Rogue rivers. First spawning occurs at 15 years for males and 17 years for females. Female green sturgeon are thought to spawn only every 5 years. Adults migrate into rivers to spawn from April to July with a May to June peak. Eggs are spawned among rocky bottom substrates and juveniles spend 1 to 4 years in freshwater.

Green Sturgeon, Endangered Species Act (ESA),
2009William H. Satterthwaite, Michael P. Beakes, Erin M. Collins, David R. Swank, Joseph E. Merz, Robert G. Titus, Susan M. Sogard, Marc Mangel Steelhead Life History on California’s Central Coast: Insights from a State-Dependent Model

Steelhead Oncorhynchus mykiss display a dizzying array of life history variation (including the purely resident form, rainbow trout). We developed a model for female steelhead in coastal California (close to the southern boundary of their range) in small coastal streams. We combined proximate (physiological) and ultimate (expected reproductive success) considerations to generalize the notion of a threshold size for emigration or maturity through the development of a state-dependent life history theory. The model involves strategies that depend on age, size or condition, and recent rates of change in size or condition during specific periods (decision windows) in advance of the actual smolting or spawning event. This is the first study in which such a model is fully parameterized based on data collected entirely from California steelhead populations, the majority of data coming from two watersheds the mouths of whose rivers are separated by less than 8 km along the coast of Santa Cruz County. We predicted the occurrence of resident life histories and the distribution of sizes and ages at smolting for steelhead rearing in the upstream habitats of these streams. We compared these predictions with empirical results and show that the theory can explain the observed pattern and variation.

Steelhead, Life History,
2001National Marine Fisheries Service (NMFS)Endangered and Threatened Species: Final Listing Determination for Klamath Mountains Province Steelhead180102

In keeping with a recent Federal Court ruling, NMFS has reconsidered the status of Klamath Mountains Province (KMP) steelhead Evolutionarily Significant Unit (ESU) under the Endangered Species Act of 1973 (ESA), as amended. After reviewing the best available scientific and commercial information, NMFS has determined that KMP steelhead do not warrant listing as threatened or endangered at this time.

Steelhead, Endangered Species Act (ESA),
2006C.W. HuntingtonEstimates of anadromous fish runs above the site of Iron Gate Dam, 18010203

The following memorandum is intended to provide updates on two elements of work that has been done to estimate the potential for anadromous fish production above the site of Iron Gate Dam (IGD). These elements include:
􀂃 Preliminary estimates of the historic potential for chinook production above Upper Klamath Lake (UKL) that were included in a technical memo I submitted to you in April 2004.
􀂃 Estimates of historic and recently suitable habitat for anadromous fish in streams within the drainage basin above IGD.

Anadromous fish, Iron Gate Dam (IGD), Upper Klamath, Chinook Salmon
1998James S. HopelainıAge, Growth, and Lief History of Klamath River Basin Steelhead Trout (Oncorhynchus mykiss irideus) as Determined from Scale Analysis180102

AduIt steeIhead (Oncorhynchus mykiss irideus) scales were analyzed from eight fall-run, two spring-run, and one winter-run stocks within the Klamath-Trinity River system, from 1981 through 1983, to provide basic information on age, growth, and life history. The higher degree of half-pounder occurrence of upper KIamath River steelhead stocks (86.7 to 100%) compared to Trinity River steelhead stocks (32.0 to 80.0%) was the major life history difference noted in scale analysis. Early life history was similar for all areas sampled with most juveniles (86.4%) remaining in freshwater during the first two years of life before migrating to sea. Repeat spawning ranged from 17.6 lo 47.9% for fall-run, 40.0 to 63.6% for spring-run, and 31.1% for winter-run steelhead. Mean length of adults at first spawning was inversely related to percent half-pounder occurrence in each stock. Ages of returning spawners, back calculated lengths at various life stages, and growth information are presented.

Steelhead, Life History, Scale Analysis
1966John D. Fortune Jr, Arthur R. Gerlach, C. J. HanelA Study to Determine the Feasibility of Establishing Salmon and Steelhead in the Upper Klamath Basin, , , , 180102

Published reports and personal interviews indicate that chinook salmon were present in the Mid- and Upper-Klamath Basin during the months of September, October and November, until the early 1900's. A photograph
substantiates the presence of chinook salmon in Link River. These runs were first curtailed around 1889-1902 when log crib dams were constructed near Klamathon by the Klamath River Improvement and Lumber
Company. These dams, constructed with no or inadequate fish ladders, seriously limited the migrations of salmon into the Upper Basin, and in 1910 the Bureau of Fisheries installed its racks a t Klamathon, further curtailing them. In 1917, the construction of Copco Dam formed a complete block to upstream migration. The Power Company constructed a fish hatchery on Fall Creek below Copco 82 Dam, at the request of the California Department of Fish and Game Commission, to mitigate for the loss of upstream production.

Because of difficulty in differentiating steelhead from large rainbow trout , accurate information on the history of steelhead migrations was impossible to obtain. It can be said that an intrastream migration of large rainbow trout or sen run steelhead did occur, appearing in the Upper Cash in the fall and again in the spring. An intrastream migration of resident rainbows now occurs during the spring. In the section of the Klamath River from the Frain Ranch (River m i l e 217) to Klamath Lake area and from Klamath Lake up the Williamson-Sprague River systems. A smaller migration occurs in the fall in the Klamath River upstream over the J. C. Boyle fish ladder.

Chinook salmon, Steelhead, Rainbow trout,
1994Busby, P. J., T. C. Wainwright, R. S. WaplesStatus Review for Klamath Mountains Province Steelhead, , , 180102

The Endangered Species Act (ESA) allows listing of "distinct population segments" of vertebrates as well as named species and subspecies. The policy of the National Marine Fisheries Service (NMFS) on this issue for Pacific salmon and steelhead is that a population will be considered "distinct" for purposes of the ESA if it represents an Evolutionarily Significant Unit (ESU) of the species as a whole. To be considered an ESU, a population or group of populations must 1) be substantially reproductively isolated from other populations, and 2) contribute substantially to ecological/genetic diversity of the biological species. Once an ESU is identified, a variety of factors related to population abundance are considered in determining whether a listing is warranted. NMFS received a petition in May 1992 asking that winter steelhead of Oregon's Illinois River be listed as a threatened or endangered species under the ESA. In May 1993, NMFS published a Federal Register notice concluding that Illinois River winter steelhead did not by themselves constitute a species as defined by the Endangered Species Act (ESA). At the same time, NMFS indicated that it would undertake a broader status review to determine the boundaries of the Evolutionarily Significant Unit (ESU) that contains Illinois River winter steelhead and determine whether this broader group was threatened or endangered. This report summarizes biological and environmental information gathered in that status review.

Based on genetic, life history, zoogeographic, geologic, and environmental information, we conclude that the ESU that contains Illinois River winter steelhead extends from the vicinity of Cape Blanco in southern Oregon to the Klamath River Basin (inclusive) in northern California. These are essentially the boundaries of a prominent geologic feature known as the Klamath Mountains Province.

Endangered Species Act (ESA), Redband trout, rainbow trout
2007Russell F. Thurow, Bruce E. Rieman, Danny C. Lee, Philip J. Howell, Raymond D. PerkinsonDistribution and Status of Redband Trout in the Interior Columbia River Basin and Portions of the Klamath River and Great Basins180102

We summarized existing knowledge (circa 1996) of the potential historical range and the current distribution and status of non-anadromous interior redband trout Oncorhynchus mykiss ssp. in the U.S. portion of the interior Columbia River Basin and portions of the Klamath River and Great Basins (ICRB). We estimated that the potential historical range included 5,458 subwatersheds and represented about 45% of the species’ North American range. Two forms of interior redband trout were considered, those sympatric with steelhead Oncorhynchus mykiss ssp. and allopatric forms that evolved outside the range of steelhead. Data were compiled from existing surveys and expert opinions of over 150 biologists during the scientific assessment for the Interior Columbia River Basin Ecosystem Management Project (ICBEMP). We also predicted fish presence and status in unsampled areas, using statistical models to quantitatively explore relationships among redband trout status and distribution, the biophysical environment, and land management. Redband trout had the highest likelihood of being present or supporting strong populations in mid-size or smaller streams, of higher gradients, in highly erosive landscapes with steep slopes, with more solar radiation, and mean annual air temperatures less than 8–9ºC. Variables reflecting the degree of human disturbance within watersheds (road density, land ownership, and management emphasis) were also important. Redband trout remain the most widely distributed native salmonid in the ICBEMP assessment area and the second most widely distributed native fish, occupying 47% of the subwatersheds and 64% of their potential range. Sympatric redband trout are the most widely distributed of the two forms, present in an estimated 69% of their potential range.

Redband Trout, Distribution, Conservation, Restoration
2004K. J. Rodnick, A. K. Gamerl, K. R. Lizars, M.T. Bennett, R. N. Rausch, E. R. KeeleyThermal tolerance and metabolic physiology among redband trout populations in south-eastern Oregon,

Streamside measurements of critical thermal maxima (Tcrit), swimming performance (Ucrit), and routine (Rr) and maximum (Rmax) metabolic rates were performed on three populations of genetically distinct redband trout Oncorhynchus mykiss in the high-desert region of south-eastern Oregon. The Tcrit values (29401 C) for small (40–140 g) redband trout fromthe three streams, and large (400–1400 g) redband trout at Bridge Creek were not different, and were comparable to published values for other salmonids. At high water temperatures (24–28 C), large fish incurred higher metabolic costs and were more thermally sensitive than small fish. Ucrit (3601 LF s1), Rr (20013 mg O2 kg0830 h1) and metabolic power (53322 mg O2 kg0882 h1) were not significantly different between populations of small redband trout at 24 C. Rmax and metabolic power, however, were higher than previous measurements for rainbow trout at these temperatures. Fish from Bridge Creek had a 30% lower minimum total cost of transport (Cmin), exhibited a lower refusal rate, and had smaller hearts than fish at 12-mile or Rock Creeks. In contrast, no differences in Ucrit or metabolism were observed between the two size classes of redband trout, although Cmin was significantly lower for large fish at all swimming speeds. Biochemical analyses revealed that fish from 12-mile Creek, which had the highest refusal rate (36%), were moderately hyperkalemic and had substantially lower circulating levels of free fatty acids, triglycerides and albumin. Aerobic and anaerobic enzyme activities in axial white muscle, however, were not different between populations, and morphological features were similar.

Redband trout, Thermal and Metabolic Physiology, Morphology, Water Temperature
2016Brooke E. Penaluna, Alicia Abadía-Cardoso, Jason B. Dunham, Francisco J. García-Dé León, Robert E. Gresswell, Arturo Ruiz Luna, Eric B. Taylor, Bradley B. Shepard, Robert Al-Chokhachy, Clint C. Muhlfeld, Kevin R. Bestgen, Kevin Rogers, Marco A. Escalante, Ernest R. Keeley, Gabriel M. Temple, Jack E. Williams, Kathleen R. Matthews, Ron Pierce, Richard L. Mayden, Ryan P. Kovach, John Carlos Garza, Kurt D. FauschConservation of Native Pacific Trout Diversity in Western North America, ,

Pacific trout Oncorhynchus spp. in western North America are strongly valued in ecological, socioeconomic, and cultural views, and have been the subject of substantial research and conservation efforts. Despite this, the understanding of their evolutionary histories, overall diversity, and challenges to their conservation is incomplete. We review the state of knowledge on these important issues, focusing on Pacific trout in the genus Oncorhynchus. Although most research on salmonid fishes emphasizes Pacific salmon, we focus on Pacific trout because they share a common evolutionary history, and many taxa in western North America have not been formally described, particularly in the southern extent of their ranges. Research in recent decades has led to the revision of many hypotheses concerning the origin and diversification of Pacific trout throughout their range. Although there has been significant success at addressing past threats to Pacific trout, contemporary and future threats represented by nonnative species, land and water use activities, and climate change pose challenges and uncertainties. Ultimately, conservation of Pacific trout depends on how well these issues are understood and addressed, and on solutions that allow these species to coexist with a growing scope of human influences.

Pacific trout, Conservation, Pacific Trout Diversity,
2012Amy L. Haak, Jack E. WilliamsSpreading the Risk: Native Trout Management in a Warmer and Less-Certain Future, ,

Management strategies that increase biological diversity and promote varied approaches to population protection are more likely to succeed during a future in which global warming drives rapid environmental change and increases uncertainty of future conditions.We describe how the concept of a diversemanagement portfolio can be applied to native trout conservation by increasing representation (protecting and restoring diversity), resilience (having sufficiently large populations and intact habitats to facilitate recovery from rapid environmental change), and redundancy (saving a sufficient number of populations so that some can be lost without jeopardizing the species). Saving diversity for native trout requires the conservation of genetically pure populations, the protection and restoration of life history diversity, and the protection of populations across the historical range. Protecting larger stronghold populations is important because such populations will have a better chance of surviving future disturbances, including those associated with climate change. The long-term persistence of populations is likely to require management for larger population sizes and larger habitat patches than currently exist for many native trout populations. Redundancy among these elements is important given that many populations are small and occupy reduced habitat in fragmented stream systems and therefore are increasingly vulnerable to extirpation. Application of the concept is further described in case studies of Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri and Rio Grande cutthroat trout O. clarkii virginalis, two subspecies that illustrate many of the challenges that are common to management of western native trout.

Salmon, Yellowstone Cutthroat Trout, Redundancy, Resilience, Rio Grand Cutthroat Trout
2012USFWSConservation Agreement for Pacific Lamprey

The Pacific Lamprey Conservation Initiative (Initiative) has been developed to promote implementation of conservation measures for Pacific Lamprey in Alaska, Washington, Oregon, Idaho, and California. The Initiative has three phases: Assessment and Template for Conservation Measures (Luzier et al. 2011); Conservation Agreement (Agreement); and Regional Implementation Plans. The Agreement represents a cooperative effort among natural resource agencies and tribes to reduce threats to Pacific Lamprey and improve their habitats and population status. Cooperative efforts through the Agreement intend to: a) develop regional implementation plans derived from existing information and plans; b) implement conservation actions; c) promote scientific research; and d) monitor and evaluate the effectiveness of those actions.

The strategies and schedules for implementing conservation actions by region will be described in the regional implementation plans. In regions that are early in the planning process, the work will focus on identification of ongoing and needed actions. In other regions that have already gone through an extensive planning process, the focus will be on prioritizing actions, identifying potential funding and developing schedules for implementation. For example, in the Columbia River region the implementation plans would rely heavily on the threats and the proposed actions identified in the Tribal Pacific Lamprey Restoration Plan for the Columbia River (2011), Army Corps of Engineers 10- year Passage Plan for Lamprey (2009), the U.S. Bureau of Reclamation Lamprey Assessment (2011), and the U.S. Fish and Wildlife Service (USFWS) Assessment and Template for Conservation Measures (Luzier et al. 2011)

Pacific Lamprey, Entosphenus tridentatus, Conservation actions,
2015Damon H. Goodman, Stewart B. Reid, Nicholas A. Som, William R. PoytressThe punctuated seaward migration of Pacific lamprey (Entosphenus tridentatus): environmental cues and implications for streamflow management,

We investigated emigration timing of juvenile Pacific lamprey (Entosphenus tridentatus) over a 10-year period in the Sacramento River, California, USA. Emigration was punctuated with 90% of macrophthalmia in daily catches of at least 50 individuals. Macrophthalmia were observed primarily between November and May, with among-year variation in median emigration date over four times that of sympatric anadromous salmon. Our best model associating catch and environmental factors included days from rain event, temperature, and streamflow. We found strong evidence for an association of catch with days from rain events, a surrogate for streamflow, with 93% of emigrants caught during an event and the two subsequent days. Emigration was more likely during nighttime during subdaily sampling after accounting for the effects of factors significantly associated with daily catch. These results emphasize the importance of natural variation in streamflow regimes and provide insight for management practices that would benefit emigrating lampreys, such as synchronizing dam releases with winter and spring storms to reduce migration time, timing diversions to avoid entrainment during emigration windows, and ensuring streamflows are sufficient to reach the ocean, thereby avoiding mass stranding events.

Pacific Lamprey, Entosphenus tridentatus, Streamflow management
2017Damon H. Goodman, Stewart B. Reid, Rene C. Reyes, Brandon J. Wu, Brent B. BridgesScreen Efficiency and Implications for Losses of Lamprey Macrophthalmia at California’s Largest Water Diversions

We investigated the guidance efficiency of fish screens for the protection of emigrating Pacific Lamprey Entosphenus tridentatus and Western River Lamprey (also known as River Lamprey) Lampetra ayresii in a series of experimental trials. All trials were conducted at the Tracy Fish Collection Facility, located in the Sacramento– San Joaquin River Estuary at the entrance to one of the world’s largest surface water diversions. Using 1,200 lamprey macrophthalmia, we tested for the effect of screen type, time of day, and channel water velocity to guide their swimming behavior to avoid entrainment. We found overwhelming evidence for an effect of screen type on efficiency, whereby all lampreys were successfully guided to a holding tank when a vertical traveling screen was used. This was likely due to the small pore size of the screen relative to lamprey sizes. In contrast, the efficiency of louvers, a behavioral screen designed for salmonids, varied by the interaction of time of day and channel velocity. During nighttime, when lamprey typically emigrate, louver guidance efficiency ranged from 21% (95% CI, 14–30%) to 24% (95% CI, 16–34%). These results were applied to estimate the probability for salvage of lamprey macrophthalmia at the Tracy Fish Collection Facility, which includes a two-stage fish screen design. Between 1957 and 2014, we estimated that 94–96% of the lampreys that were entrained in the export flows were lost and not returned to the delta. However, the probability for fish loss was reduced in 2014 when the secondary louver was replaced with a vertical traveling screen. Our results suggest that lamprey macrophthalmia entrainment into the canals will be eliminated at the Tracy Fish Collection Facility if the primary screen is converted to vertical traveling screen.

Pacific Lamprey, Entosphenus tridentatus, Western River Lamprey, River Lamprey,
2015Damon H. Goodman, Stewart B. ReidRegional Implementation Plan for Measures to Conserve Pacific Lamprey (Entosphenus tridentatus), California – South Central Coast Regional Management Unit

Pacific Lamprey, Entosphenus tridentatus, were historically widely distributed from Mexico north along the Pacific Rim to Japan. They are culturally important to indigenous people throughout their range, and play a vital role in the ecosystem: cycling marine nutrients, passing primary production up the food chain as filter feeding larvae, promoting bioturbation in sediments, and serving as food for many mammals, fishes and birds. Recent observations of substantial declines in the abundance and range of Pacific Lamprey have spurred conservation interest in the species, with increasing attention from tribes, agencies, and others.

In 2003 the U.S. Fish and Wildlife Service (USFWS) was petitioned by 11 conservation groups to list four species of lamprey in Oregon, Washington, Idaho, and California, including the Pacific Lamprey, under the Endangered Species Act (ESA) (Nawa et al. 2003). The USFWS review of the petition indicated a likely decline in abundance and distribution in some portions of the Pacific Lamprey's range and the existence of both long-term and proximate threats to this species, but the petition did not provide information describing how the portion of the species’ petitioned range (California, Oregon, Idaho, and Washington) or any smaller portion is appropriate for listing under the ESA. The USFWS was therefore unable to define a listable entity based on the petition and determined Pacific Lamprey to be ineligible for listing (USFWS 2004).

Other threatened fishes, Water Quality, Upper Klamath, Lower Klamath, Contaminants, Pacific Lamprey, Entosphenus tridentatus, Conservation measures, Limiting factors
2002David A. Close, Martin S. Fitzpatrick, Hiram W. LiThe Ecological and Cultural Importance of a Species at Risk of Extinction, Pacific Lamprey

The cultural and ecological values of Pacific lamprey (Lampetra tridentata) have not been understood by Euro-Americans and thus their great decline has almost gone unnoticed except by Native Americans, who elevated the issue and initiated research to restore its populations, at least in the Columbia Basin. They regard Pacific lamprey as a highly valued resource and as a result ksuyas (lamprey) has become one of their cultural icons. Ksuyas are harvested to this day as a subsistence food by various tribes along the Pacific coast and are highly regarded for their cultural value. Interestingly, our review suggests that the Pacific lamprey plays an important role in the food web, may have acted as a buffer for salmon from predators, and may have been an important source of marine nutrients to oligotrophic watersheds. This is very different from the Euro- American perception that lampreys are pests. We suggest that cultural biases affected management policies.

Ecological Importance, Cultural Importance, Pacific lamprey, Lampetra tridentata, Spawning migration, Conservation
2010State of California North Coast Regional Water Quality Control BoardFinal Staff Report for the Klamath River Total Maximum Daily Loads (TMDLs) Addressing Temperature, Dissolved Oxygen, Nutrient and Microcystin Impairments in California the Proposed Site Specific Dissolved Oxygen Objectives for the Klamath River in California, and the Klamath River and Lost River Implementation Plans, , , , , 180102

Final Staff Report for the Klamath River Total Maximum Daily Loads (TMDLs) Addressing Temperature, Dissolved Oxygen, Nutrient and Microcystin Impairments in California the Proposed Site Specific Dissolved Oxygen Objectives for the Klamath River in California, and the Klamath River and Lost River Implementation Plans.

Total Maximum Daily Loads (TMDLs), Microcystin impairments, dissolved oxygen
2017California Department of Fish and WildlifeState and Federally Listed Endangered and Threatened Animals of California,

This is a list of animals found within California or off the coast of the State that have been classified as Endangered or Threatened by the California Fish & Game Commission (state list) or by the U.S. Secretary of the Interior or the U.S. Secretary of Commerce (federal list). The federal agencies responsible for listing are the U.S. Fish and Wildlife Service (USFWS) and the National Marine Fisheries Service (NMFS).

The official California listing of Endangered and Threatened animals is contained in the California Code of Regulations, Title 14, Section 670.5. The official federal listing of Endangered and Threatened animals is published in the Federal Register, 50 CFR 17.11. The California Endangered Species Act of 1970 created the categories of “Endangered” and “Rare.” The California Endangered Species Act of 1984 created the categories of “Endangered” and “Threatened.” On January 1, 1985, all animal species designated as “Rare” were reclassified as “Threatened.”

Also included on this list are animal “Candidates” for state listing and animals “Proposed” for federal listing; federal “Candidates” are currently not included. A state Candidate species is one that the Fish and Game Commission (FGC) has formally declared a candidate species. A federal Proposed species is one that has had a published proposed rule to list in the Federal Register.

Endangered and Threatened species,
2012Nicole Athearn, Daryl Van Dyke, Joel Shinn, Matt Barry, Rick Kearney, Steve Morey, William Kendall, Kurt Rinehart, Nancy Finley, Laurie Sada, Erin Williams, Gary Curtis, Jason Cox, Laura Finley, Nick Hetrick, Dave Mauser, Josh Rasmussen, Trisha RoningerStructured Decision Making for the Selection of Surrogate Species: A Case Study in the Klamath River Watershed A Case Study…, , 180102

The U. S. Fish and Wildlife Service (FWS; Service) released its Draft Guidance for Selecting Species for Design of Landscape-scale Conservation (hereafter Guidance; USFWS, 2012) in July 2012 to provide guidance for directing Strategic Habitat Conservation towards achieving and maintaining functional landscapes. Beginning in the summer of 2012, scientists and managers from three Klamath field offices in Arcata and Yreka, California and Klamath Falls, Oregon came together with those from the Klamath National Wildlife Refuge complex in Tulelake, California and the Pacific Southwest regional office in Sacramento, California to define conservation objectives for a functional landscape in the Klamath River watershed and to pilot a surrogate species selection process at a USFWS/USGS Structured Decision Making (SDM) workshop at the FWS National Conservation Training Center. Our workshop problem statement was: We are using the process of Strategic Habitat Conservation in conjunction with a surrogate species approach to develop innovative and strategic approaches to species and ecosystem conservation in the Klamath River watershed.

Strategic Habitat Conservation, Structured Decision Making, Surrogate Species, Decision Analysis
1996Trihey & Associates, IncInstream Flow Requirements For Tribal Trust Species in the Klamath River, , , , 180102

The Yurok People have long depended on the fish resources of the Klamath River. For centuries, the Klamath River provided fish throughout the year to meet the needs of the Yurok Tribe as well as the Karuk, Hoopa and Klamath Tribes. The river is still central to the everyday lives of the Yurok People. Historically, adult salmon and steelhead returning each year to spawn, including spring and fall chinook salmon, coho salmon and steelhead, probably numbered more than one million fish. At this time large numbers of eulachon, lamprey and green sturgeon also inhabited the river. These fish were harvested for cultural, subsistence and commercial purposes. They are referred to in the report as the Yurok Tribal Species.

Tribal Trust Species, Streamflow requirements, eulachon, lamprey, green sturgeon, salmon, steelhead
2006M. F. Willson, R. H. Armstrong, M. C. Hermans, K KoskiEulachon: A Review of Biology and an Annotated Bibliography

This review and annotated bibliography was stimulated by the realization that while eulachon are an important forage fish, they are also under-studied. Historically, eulachon have had relatively little commercial value, compared to more widely known species such as herring. However, this oil-rich little fish has had an important role in the culture of Natives on the coast of southeast and south-central Alaska, and First Nations on the cost of British Columbia. Eulachon ‘grease’ was a major item of trade with Natives of Interior Alaska, as well as an important food source for coastal peoples. Subsistence use of eulachon continues, at least in some areas.
By the 1990s, the value of eulachon spawning runs to many wildlife species began to draw increased scientific attention, including several new studies of eulachon biology per se. Nevertheless, much remains to learn, not only about eulachon biology, but also about the ecological patterns and consequences for the predators of eulachon.

The authors of this review hope that it will help stimulate research on the ecology and evolution of eulachon and their predators. This review was completed in the fall of 2003. References from fall 2003 to date are listed in an addendum at the end of this manuscript.

Eulachon, Taxonomy, Distribution, Morphology
2010Richard G. Gustafson, Michael J. Ford, David Teel, Jonathan S. DrakeStatus Review of Eulachon (Thaleichthys pacificus) in Washington, Oregon, and California

On 27 November 2007, the National Marine Fisheries Service (NMFS) received a petition seeking to list southern eulachon (Thaleichthys pacificus), as a threatened or endangered species under the Endangered Species Act (ESA) of 1973. NMFS evaluated the petition to determine whether the petitioner provided substantial information as required by the ESA to list a species. Additionally, NMFS evaluated whether information contained in the petition might support the identification of a distinct population segment (DPS) that may warrant listing as a species under the ESA. NMFS determined that the 27 November 2007 petition did present substantial scientific and commercial information, or cited such information in other sources, that the petitioned action may be warranted and, subsequently, NMFS initiated an updated status review of eulachon in Washington, Oregon, and California.

The Eulachon Biological Review Team (BRT)—consisting of scientists from the Northwest Fisheries Science Center, Alaska Fisheries Science Center, Southwest Fisheries Science Center, U.S. Fish and Wildlife Service, and U.S. Forest Service—was formed by NMFS, and the team reviewed and evaluated scientific information compiled by NMFS staff from published literature and unpublished data. Information presented at a public meeting in June 2008 in Seattle, Washington, and data submitted from state agencies and other interested parties were also considered. The BRT also reviewed additional information submitted to the ESA Administrative Record.

Eulachon, Thaleichthys pacificus, Eulachon Biological Review Team (BRT),
2008Thomas H. Williams, Brian C. Spence, Walt Duffy, Dave Hillemeier, George Kautsky, Tom E. Lisle, Mike McCain, Thomas E. Nickelson, Ethan Mora, Tom PearsonFramework for Assessing Viability of Threatened Coho Salmon in the Southern Oregon/Northern California Coast Evolutionarily Significant Unit

This report describes a framework for assessing coho salmon population viability that includes developing objective, measurable criteria that when met, would define when the Southern Oregon/Northern California Coast Coho Salmon Evolutionarily Significant Unit (ESU) is naturally self-sustaining with a low risk of extinction. Technical recovery planning for Pacific salmon and steelhead is intended to produce biologically based viability criteria for listed ESUs that will be considered in setting recovery goals. The listing unit for Pacific salmon is the ESU. ESUs are defined as a population or group of populations that are substantially reproductively isolated from other conspecific population units and that represent an important part of the evolutionary legacy of the species. The Southern Oregon/Northern California Coast (SONCC) Coho Salmon ESU includes coho salmon populations from Elk River (Oregon) in the north to Mattole River (California) in the south. This report provides a framework to assess the viability of individual populations within this region and describes the spatial configuration of viable independent populations and dependent populations that would lead to a high likelihood of long-term ESU persistence. This report constitutes a technical recommendation by the TRT intended to assist recovery planners in developing recovery strategies and prioritizing recovery actions. It does not constitute official agency policy.

Coho Salmon, Southern Oregon/Northern California Coast (SONCC), Evolutionarily Significant Unit (ESU), Population Viability,
2010NOAAFBiological Opinion: Operation of the Klamath Project between 2010 and 2018, , , , , , , , , 180102

Today, the Klamath basin’s hydrologic system consists of a complex of inter-connected rivers, lakes, marshes, dams, diversions, wildlife refuges, and wilderness areas. Alterations to the natural hydrologic system began in the late 1800s, accelerating in the early 1900s, including water diversions by private water users, water diversions by the Klamath Project operated by Reclamation, and by several hydroelectric dams operated by a private company, PacifiCorp. The first PacifiCorp development was constructed in 1918 (Copco Dam) on the Klamath and it operated under a 50-year license issued by the Federal Energy Regulatory Commission (FERC) until the license expired in 2006. Although Reclamation’s Link River Dam and PacifiCorp’s Keno Dam currently have fish ladders, none of PacifiCorp’s dams were constructed with fish ladders sufficient to pass anadromous fish and, as a result, salmon and steelhead have effectively been blocked from accessing the upper reaches of the basin for close to a century. Beginning in 1956, Iron Gate Reservoir (the lowest dam in the system) flow releases were generally governed by guidelines outlined within the FERC license, commonly referred to as “FERC minimum flows.” FERC’s original license to PacifiCorp to operate its hydroelectric project on the Klamath River never underwent Endangered Species Act (ESA) consultation.

After reviewing the current status of SONCC coho salmon and its critical habitat, the environmental baseline for the action area, the effects of the Project and the cumulative effects, it is NMFS’ biological opinion that the action, as proposed, is likely to jeopardize the continued existence of SONCC coho salmon, and is likely to destroy or adversely modify SONCC coho salmon designated critical habitat.

SONCC, Coho Salmon, Risk of Extinction, Environmental Baseline, Critical Habitat, Hydrologic system
2002California Department of Fish and GameStatus review of California Coho Salmon North of San Francisco

On July 28, 2000, the Fish and Game Commission (Commission) received a petition to list coho salmon north of San Francisco as an endangered species under provisions of the California Endangered Species Act (CESA). The Commission referred the petition to the Department of Fish and Game (Department) on August 7, 2000, for evaluation. The Department found that the information in the petition was sufficient to indicate the action may be warranted and recommended the Commission accept the petition. The petition was accepted by the Commission on April 5, 2001. On April 27, 2001 the Commission published a Notice of Findings in the California Regulatory Notice Register declaring coho salmon a candidate species, thereby starting the candidacy period.

This report contains the results of the Department’s status review and recommendations to the Commission. The Department evaluated the status separately for the two coho salmon Evolutionarily Significant Units (ESU) that occur in California: Southern Oregon/Northern California Coast Coho ESU (SONCC Coho ESU - those populations from Punta Gorda north to the Oregon border) and the Central California Coast Coho
ESU (CCC Coho ESU - those populations from San Francisco Bay north to Punta Gorda).

The Department concludes that the listing of the California portion of the SONCC Coho ESU as endangered is not warranted, but listing as threatened is warranted. The Department recommends that the Commission add coho salmon north of Punta Gorda to the list of threatened species. The Department concludes that coho salmon in the CCC Coho ESU is in serious danger of becoming extinct throughout all or a significant portion of its range. The Department concludes that listing this species as an endangered species is warranted. The Department recommends that the Commission add coho salmon north of, and including, San Francisco Bay to Punta Gorda to the list of endangered species.

Coho Salmon, California Endangered Species Act (CESA), Evolutionarily Significant Units (ESU), Central California Coast Coho ESU (CCC Coho ESU)
1994Larry R. Brown, Peter B. Moyle, Ronald M. YoshiyamaHistorical Decline and Current Status of Coho Salmon in California

The southernmost populations of coho salmon Oncorhynchus kisutch occur in California where native coho stocks have declined or disappeared from a1l streams in which they were historically recorded. Coho salmon previously occurred in as many as 582 streams, from the Smith River near the Oregon border to the San Lorenzo River on the central coast. Information on the recent presence or absence of coho salmon was available for only 248 (43%) of those streams. Of these 248 streams, 54% still contained coho salmon and 46% did not. The farther south a stream is located, the more likely it is to have lost its coho salmon population. We estimate that the total number of adult coho salmon entering California streams in 1987-1991 averaged around 31,000 fish per year, with hatchery populations making up 57% of this total. Thus, about 13,000 nonhatchery coho salmon have been spawning in California streams each year since 1987, an estimate that includes naturalized stocks containing about 9,000 fish of recent hatchery ancestry. There are now probably less than 5,000 native coho salmon (with no known hatchery ancestry) spawning in California each year, many of them in populations ofless than 100 individuals. Coho populations today are probably less than 6% of what they were in the 1940s, and there has been at least a 70% decline since the 1960s. There is every reason to believe that California coho populations, including hatchery stocks, will continue to decline. The reasons for the decline of coho salmon in California include: stream alterations brought about by poor land-use practices (especially those related to logging and urbanization) and by the effects of periodic floods and drought, the breakdown of genetic integrity of native stocks, introduced diseases, overharvest, and climatic change. We believe, that ,coho salmon in California qualify for listing as a threatened species under state law, and certain populations maybe threatened or endangered under federal law.

Coho Salmon, Historical Decline, Threatened species
1930John O. SnyderFish Bulletin No. 34. Salmon of the Klamath River California. I. The Salmon and the Fishery of Klamath River. II. A Report on the 1930 Catch of King Salmon in Klamath River180102

The present paper is a digest of the work accomplished in a salmon investigation conducted under the authority of the Bureau of Commercial Fisheries of the California Division of Fish and Game. Active work was begun in 1919, and is still in progress. At the outset the investigation was so planned as to contribute as directly as possible to the solution of certain questions relating to the conservation of the fishery. The work has progressed in a fairly satisfactory way in some directions as will appear, while in others the results are not so good. The information now most needed relates to the seaward migration of young salmon, and to the relative contribution of natural and artificial propagation to the population of the river. It may seem that the matter of depletion is overstressed in this report, since its progress has been evident for years. A condition of increasing depletion was not sufficiently evident on the Klamath however, to be convincing to those most interested. In fact, opinions to the contrary were commonly held, some asserting that the "run" was not only maintaining itself but that it was gradually building up. There is very little exact information concerning fishing operations on Klamath River previous to 1912, and no really dependable statistics are available relating to the catch before that time. During the period of placer mining on the river, large numbers of salmon were speared or otherwise captured on or near their spawning beds, and if credence is given to the reports of old miners, there then appeared the first and perhaps major cause of early depletion. In 1912 three plants operated on or near the estuary and the river was heavily fished, no limit being placed on the activities of anyone.

Salmon, Fishing Operations,
2016Russell W. Perry, John M. Plumb, Nicholas A. Som, Nicholas Hetrick, Thomas Hardy Modeling Infection and Mortality of Juvenile Chinook Salmon due to Disease caused by Ceratonova Shasta in the Klamath River180102

Disease can often shape population dynamics but complex host-parasite interactions can be difficult to incorporate into life cycle models. Juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Klamath River become infected with the myxozoan parasite Ceratonova shasta when the polychaete worm Manayunkia speciosa releases actinospores into the water column. In the Klamath River, disease prevalence and actinospore concentrations have been routinely monitored since 2005, providing information about population-level disease prevalence. Concurrently, sentinel experiments with fish held in-river for a known duration have revealed that mortality increases with spore concentration and temperature. We developed statistical models to relate rates of infection and mortality to spore concentrations and temperature. We then incorporated these models into a dynamic life-cycle simulation model to understand how migration and exposure of juvenile Chinook salmon influences the magnitude and location of their mortality in the Klamath River. This model provides an estimate of disease-related mortality at the population-level, which can then be incorporated as a life-stage transition probability in a broader life-cycle model.

Chinook salmon, Ceratonova shasta, Disease-related mortality, Klamath River
2016CDFGKlamath River Basin Fall Chinook Salmon Spawner Escapement, In-river Harvest and Run-size Estimates, 1978-2016180102

Klamath River Basin Fall Chinook Salmon Spawner Escapement, In-river Harvest and Run-size Estimates, 1978-2016

Fall Chinook Salmon, Spawner Escapement,
2011Peter B. Adams, L.B. Boydstun, Sean P. Gallagher, Michael K. Lacy, Trent McDonald, Kevin E. ShafferFish Bulletin 180 California Coastal Salmonid Population Monitoring: Strategy, Design and Methods,

California’s salmon and steelhead populations have experienced marked declines leading to listing of almost all of California’s anadromous salmonids under the California Endangered Species Act (CESA) and Federal Endangered Species Act (ESA). Both CESA and ESA listings require recovery plans that call for monitoring to provide some measure of progress toward recovery. In addition, there are related monitoring needs for other management activities such as hatchery operations and fisheries management.

This California Coastal Salmonid Monitoring Plan (CMP) has been developed to meet these monitoring needs, describing the overall strategy, design, and methods used in monitoring salmonid populations. Implementation details of the plan are described in Shaffer (in prep.). The CMP uses the Viable Salmonid Population concept as the framework for plan development. The VSP conceptual framework assesses salmonid viability in terms of four key population characteristics: abundance, productivity, spatial structure, and diversity. High abundance buffers a population against both ‘normal’ and catastrophic variation due to environmental conditions and loss due to anthropogenic factors. High productivity will lead to more certain replacement when populations are placed under either natural or anthropogenic stress. Wide spatial structure reduces extinction risk due to catastrophic events and provides pathways for recolonization. Diversity in life history traits (e.g., time of spawning, juvenile life history, adult fish size, age structure, degree of anadromy, etc.) provides resilience against extinction risk from changing conditions.

California Coastal Salmonid Monitoring Plan (CMP), Endangered Species Act (ESA), California Coho Salmon Recovery Strategy,
2015US Fish and Wildlife ServiceKlamath Recovery Unit Implementation Plan for Bull Trout (Salvelinus confluentus), , , 180102

This recovery unit implementation plan (RUIP) describes the threats to bull trout (Salvelinus confluentus) and the site-specific management actions necessary for recovery of the species within the Klamath Recovery Unit, including estimates of time required and cost. This document supports and complements the Recovery Plan for the Coterminous U.S. Population of Bull Trout (USFWS 2015a), which describes recovery criteria and a general range-wide recovery strategy for the species. Detailed discussion of species status and recovery actions within each of the six recovery units is provided in six RUIPs that have been developed in coordination with State, Federal, Tribal, and other conservation partners. This document incorporates our responses to public comment on the Draft Klamath RUIP (USFWS 2015b) received during the comment period from June 4 to July 20, 2015

Implementation Plan, Klamath Recovery Unit, Bull trout, Recovery Unit Implementation Plan (RUIP), Brown trout,
2014U.S. Fish and Wildlife ServiceRevised Draft Recovery Plan for the Coterminous United States Population of Bull Trout (Salvelinus confluentus), ,

Our most recent 5-year status review for bull trout was completed on April 8, 2008, and concluded that listing the species as “threatened” remained warranted range-wide in the coterminous United States. Based on this status review, in our most recent recovery report to Congress (USFWS 2012) we reported that bull trout were generally “stable” overall range-wide (species status neither improved nor declined during the reporting year), with some core area populations decreasing, some stable, and some increasing. Since the listing of bull trout, there has been very little change in the general distribution of bull trout in the coterminous United States, and we are not aware that any known, occupied bull trout core areas have been extirpated. Additionally, since the listing of bull trout, numerous conservation measures have been and continue to be implemented across its coterminous range. These measures are being undertaken by a wide variety of local and regional partnerships, including State fish and game agencies, State and Federal land management and water resource agencies, Tribal governments, power companies, watershed working groups, water users, ranchers, and landowners. In many cases these bull trout conservation measures incorporate or are closely interrelated with work being done for recovery of salmon and steelhead, which are limited by many of the same threats. The Service has compiled a comprehensive overview of conservation actions and successes since 1999 for bull trout in each recovery unit that is referenced in this revised draft recovery plan.

Bull Trout, Salvelinus confluentus, Recovery Plan, Threatened species, Endangered Species Act, Strategic Plan, Threat Assessment Tool,
2010Oregon Department of Fish and WildlifeStatus Klamath Rainbow/Rainbow Trout Dams in Scenario. Klamath River Rainbow Trout Peaking Reach Klamath River, , , , 180102

The purpose of this document is to provide an outline for a presentation by ODFW staff to the expert panel on redband, rainbow and bull trout which will provide input for the secretarial determination of whether to remove the four hydroelectric dams on the Klamath River. The expert panel will evaluate if the continued operation of the four main stem hydro electric facilities is in the best interest of the people of the United States and if fisheries will benefit.

ODFW has compared a scenario of continuing to operate the Klamath Hydroelectric Project status quo with no reintroduction of anadromous fish versus removal of the four Klamath Hydroelectric dams, implementation of the KBRA and reintroduction and volitional re-colonization of anadromous fish. ODFW has extensive information on trout populations in the Klamath basin and will present information on how removal of the Klamath River dams and implementation of the Klamath Basin Restoration Agreement will effect the population of redband, rainbow, and bull trout. For redband trout ODFW answered the general questions for the expert panel and gave a brief summary of current status of the population and status of redband trout with KBRA implemented with dam removal. An outline was developed covering the major points affecting the health of rainbow and bull trout populations in the Upper Klamath Basin.

Anadromous fish, Klamath Basin, Redband trout, Rainbow trout, Bull trout, Hydroelectric dams,
2003Jason Dunham, Bruce Rieman, Gwynne ChandlerInfluences of Temperature and Environmental Variables on the Distribution of Bull Trout within Streams at the Southern Margin of Its Range, ,

The bull trout Salvelinus confluentus is believed to be among the most thermally sensitive species in coldwater habitats in western North America. We conducted a comprehensive field assessment of thermal habitat associations throughout the southern margin of the species’ range. We developed models of thermal habitat associations using two data sets representing a geographically diverse range of sites and sampling methods. In both data sets, maximum temperature was strongly associated with the distribution of bull trout. In spite of the potential biases in these data sets, model predictions were similar. In both cases, the probability of the occurrence of bull trout exceeded 50% when the maximum daily temperature was less than 14–168C, a result that is consistent with recent laboratory-based thermal tolerances. In one data set, we modeled
the association between the distribution of bull trout and environmental variables, including temperature, instream cover, channel form, substrate, and the abundance of native and nonnative salmonid fishes. Only temperature was strongly associated with the distribution of bull trout. Our results and related studies of landscape habitat associations suggest that conservation efforts for bull trout would benefit from a focus on maintaining and restoring large and interconnected coldwater habitats.

Bull trout, Environmental Variables, Thermal habitat
2016Joseph R. Benjamin, Jeannie M. Heltzel, Jason B. Dunham, Michael Heck, Nolan BanishThermal Regimes, Nonnative Trout, and Their Influences on Native Bull Trout in the Upper Klamath River Basin, Oregon, 18010206

The occurrence of fish species may be strongly influenced by a stream’s thermal regime (magnitude, frequency, variation, and timing). For instance, magnitude and frequency provide information about sublethal temperatures, variability in temperature can affect behavioral thermoregulation and bioenergetics, and timing of thermal events may cue life history events, such as spawning and migration. We explored the relationship between thermal regimes and the occurrences of native Bull Trout Salvelinus confluentus and nonnative Brook Trout Salvelinus fontinalis and Brown Trout Salmo trutta across 87 sites in the upper Klamath River basin, Oregon. Our objectives were to associate descriptors of the thermal regime with trout occurrence, predict the probability of Bull Trout occurrence, and estimate upper thermal tolerances of the trout species. We found that each species was associated with a different suite of thermal regime descriptors. Bull Trout were present at sites that were cooler, had fewer high-temperature events, had less variability, and took longer to warm. Brook Trout were also observed at cooler sites with fewer hightemperature events, but the sites were more variable and Brook Trout occurrence was not associated with a timing descriptor. In contrast, Brown Trout were present at sites that were warmer and reached higher temperatures faster, but they were not associated with frequency or variability descriptors. Among the descriptors considered, magnitude (specifically June degree-days) was the most important in predicting the probability of Bull Trout occurrence, and model predictions were strengthened by including Brook Trout occurrence. Last, all three trout species exhibited contrasting patterns of tolerating longer exposures to lower temperatures. Tolerance limits for Bull Trout were lower than those for Brook Trout and Brown Trout, with contrasts especially evident for thermal maxima.

Native Bull Trout, Nonnative Trout, Thermal influences, Brook Trout, Brown Trout,
2017Will Houston‘A cultural tragedy’: Karuk Tribe cuts salmon harvest to 200 fish Karuk Tribe cuts harvest; fishery council to finalize 2017 season rules, 180102

For the first time in its history, the Karuk Tribe will be limiting ceremonial salmon harvests for tribal members because of the record low forecast for returning Chinook salmon on the Klamath River. Karuk Tribal Chairman Russell “Buster” Attebery said in a Monday statement that it was his “saddest day as chairman” to announce the tribe will limit harvest for sustenance and ceremonial purposes to just 200 salmon. “This is the first time in our history that we have imposed limits on traditional dip net fishermen working to feed their extended families and tribal elders,” he stated.About 12,000 Chinook salmon are forecast to return to the Klamath River to spawn this year, which is a record low, according to the council. The Karuk Tribe states this year’s forecast represents about 10 percent of the average run size during the past three decades. Tribes and fishery scientists have attributed the low return to poor ocean conditions, drought and parasitic outbreaks in 2014 and 2015 that are estimated to have killed up to 90 percent of juvenile Chinook salmon in the river.

Karuk Tribe, Chinook salmon
2017Hank SimsYurok Tribe Warns of ‘Most Catastrophic Fisheries Collapse in Klamath River History’180102

The Yurok Tribe is bracing for the far-reaching economic, cultural, and social challenges created by what is expected to be the most catastrophic fisheries collapse in the Klamath River’s history. The number of fall Chinook salmon predicted to return to the river in 2017 — approximately 11,000 fish — is the lowest on record, a result of two consecutive, juvenile fish disease outbreaks and other contributing factors. The Tribe’s 2017 allocation, set by the Pacific Fisheries Management Council, will likely be about 650 fish or one fish for every 10 Tribal members. In response to the all-time low forecast, the Yurok Tribe will not have a commercial fishery for a second year in row to protect salmon stocks. This unprecedented fisheries crash will have real consequences for the Yurok people, whose traditions, lives and livelihoods are intimately connected to the Klamath River and its salmon.

A March 2016 agreement between the Tribe, States of California and Oregon, as well as dam owner PacifiCorp and other stakeholders, planned the removal of the dams by 2020. The Tribe is working hard to ensure the dam removal process continues as planned and salmon can finally return to the upper reaches of the river. If the dams are removed it will be a major step toward the restoration of the Klamath River, however it does little to address the direct social consequences attached to the looming salmon disaster.

Chinook salmon, Yurok Tribe, Fisheries collapse
2015US Fish &Wildlife ServiceTechnical Reference On Using Surrogate Species for Landscape Conservation, ,

Surrogate species have been defined as species which represent other species or aspects of the environment and are used to attain a conservation objective. Throughout the literature, one of the statements made by many authors is that the use of surrogate species is necessary. Managers cannot identify the habitat and resource needs of every species in a landscape; monitor environmental or management effects on every species; or directly monitor all of the workings, interactions and threats in the environment, so using surrogate species becomes inevitable even when it is not explicitly recognized.

Inconsistent use of the terms, concepts, and definitions of surrogate species has created challenges for evaluating their usefulness and improving their effectiveness in conservation planning. There is much confusion and misuse of surrogate species terms, even within the scientific literature. Any use of a surrogate term should be accompanied with a clear definition. The most successful applications of surrogate species share (1) explicit goals for their use, (2) a careful selection process using well-defined criteria for achieving the stated goals, and (3) well designed monitoring for testing the efficacy of the approach used. In contrast, the main impediments to using surrogate species successfully have been (1) confusing terminology, (2) unclear objectives, and (3) incorrect or ambiguous implementation. For surrogate species to be effective, the concepts, goals, methodologies and specific applications of the different types of surrogate species used need to be explicit, and their intended objectives clear and measurable.

Surrogate Species, Biodiversity Assessment, Biodiversity Indicators, Ecological Integrity, Conservation
2016NOAANOAA Fisheries Protected Resources Strategic Plan: 2016 – 2020 Conserving America’s Marine Protected Species, , , , , , ,

This plan provides national-level strategic goals for the protected species management programs across National Oceanic and Atmospheric Administration (NOAA) Fisheries (this includes Protected Resources Divisions in NOAA Fisheries’ five Regional Offices), as well as strategic goals specific to the NOAA Fisheries Headquarters Office of Protected Resources. We developed these priorities in consideration of the Office of Protected Resources’ core mission in the context of current fiscal conditions and NOAA Fisheries, NOAA, and Department of Commerce (DOC) strategic plans and priorities.

Over the next five years we will focus on four strategic goals. The goals align with and take advantage of our strengths and unique capabilities, guiding the work of Office of Protected Resources and the NOAA Fisheries protected resources management programs around the country (this includes Protected Resources Divisions in NOAA Fisheries’ five Regional Offices). We have determined our focus on these goals will make the biggest difference to our recovery and conservation mission given our expertise and current and emerging needs. The four goals are:
1. Stabilize the most critically endangered species and improve populations of those species nearing recovery
2. Develop guidelines and tools to make protected species management decisions “Climate Smart”
3. Maximize our effectiveness in implementing the ESA and MMPA
4. Cultivate collaborators to recover and conserve protected species

Endangered species, National Protected Resources Goals, Resource Management, EPA, MMPA
2015US Fish and Wildlife ServiceStrategic Plan for the U.S. Fish and Wildlife Service Fish and Aquatic Conservation Program: FY2016-2020, ,

This Strategic Plan for the U.S. Fish and Wildlife Service Fish and Aquatic Conservation Program: FY2016-2020 (Plan) is built around seven core goals:
• Conserve Aquatic Species;
• Conserve, Restore, and Enhance Aquatic Habitats;
• Manage Aquatic Invasive Species;
• Fulfill Tribal Trust and Subsistence Responsibilities;
• Enhance Recreational Fishing and Other Public Uses of Aquatic Resources;
• Increase Staffing Levels, Technical Capabilities, and Natural and Physical Assets to Fully Meet Our Mission; and
• Educate and Engage the Public and our Partners to Advance our Conservation Mission.

Each of these goals acknowledges the specific and very real challenges we face today in achieving our mission. Each goal also contains specific objectives and related strategies to address those challenges and achieve measurable conservation successes. The Plan builds upon prior FAC Strategic Plans and the recommendations of the Sport Fishing and Boating Partnership Council (SFBPC), contained in their report, Strategic Vision for Fish and Aquatic Resource Conservation in the Fish and Wildlife Service: A Partnership Perspective, and provided to the Service in July 2013. This report resulted from a collaborative visioning effort conducted by the SFBPC on behalf of the FAC program.

Conservation, Aquatic Invasive Species, Restoration
2016William D. Ruckelshaus CenterColumbia River Basin Salmon and Steelhead Long-Term Recovery Situation Assessment, ,

The Assessment Team conducted 206 semi-structured interviews with individuals selected for their knowledge of, engagement in, and/or concern for salmon recovery planning in the Basin. The overall goal of the assessment and this report is to provide a summary of key themes, issues and perspectives identified from the interviews, and to describe potential process options to better achieve desired outcomes regarding longterm salmon and steelhead recovery in the Basin. This report begins with an explanation of the assessment process, followed by a brief overview of recovery processes in the Basin. The report then presents a synthesis of information gained through the interviews, focusing on key themes. The last section presents a conceptual framework for assessing the salmon recovery system, along with key findings and process options for improving the system and addressing salmon and steelhead recovery in the long term. Supplemental information is provided in appendices.

The centers are making this assessment available to NOAA Fisheries and all other interested parties, in the hope that it helps inform discussions about longterm salmon and steelhead recovery processes in the Basin by providing options to consider, updated information, and a “bird’s eye view” of a complex policy environment the team learned few see in its entirety.

Salmon, Steelhead, Long-term Recovery, Conceptual Framework,
2016The Oregon Conservation StrategyThe Oregon Conservation Strategy, ,

The Oregon Conservation Strategy is a blueprint for conservation in Oregon. The Oregon Conservation Strategy (also referred to as the Conservation Strategy or Strategy) is an overarching state strategy for conserving fish and wildlife. It provides a shared set of priorities for addressing Oregon’s conservation needs. The Conservation Strategy brings together the best available scientific information, and presents a menu of recommended voluntary actions and tools for all Oregonians to define their own conservation role. The goals of the Conservation Strategy are to maintain healthy fish and wildlife populations by maintaining and restoring functioning habitats, preventing declines of at-risk species, and reversing declines in these resources where possible.

monitoring, conservation, habitat restoration
2013Tamara M. Wood, Susan A. Wherry, James L. Carter, James S. Kuwabara, Nancy S. Simon, Stewart A. RoundsTechnical Evaluation of a Total Maximum Daily Load Model for Upper Klamath Lake, Oregon18010206

We reviewed a mass balance model devel-oped in 2001 that guided establishment of the phosphorus total maximum daily load (TMDL) for Upper Klamath and Agency Lakes, Oregon. The purpose of the review was to evaluate the strengths and weaknesses of the model and to de-termine whether improvements could be made using information derived from studies since the model was first developed. The new data have contributed to the understanding of processes in the lakes, particularly internal loading of phos-phorus from sediment, and include measurements of diffusive fluxes of phosphorus from the bottom sediments, groundwater advection, desorption from iron oxides at high pH in a laboratory set-ting, and estimates of fluxes of phosphorus bound to iron and aluminum oxides. None of these pro-cesses in isolation, however, is large enough to account for the episodically high values of whole-lake internal loading calculated from a mass bal-ance, which can range from 10 to 20 milligrams per square meter per day for short periods.

The possible role of benthic invertebrates in lake sediments in the internal loading of phospho-rus in the lake has become apparent since the development of the TMDL model. Benthic inver-tebrates can increase diffusive fluxes several-fold through bioturbation and biodiffusion, and, if the invertebrates are bottom feeders, they can recycle phosphorus to the water column through metabol-ic excretion. These organisms have high densities (1,822–62,178 individuals per square meter) in Upper Klamath Lake. Conversion of the mean density of tubificid worms (Oligochaeta) and chi-ronomid midges (Diptera), two of the dominant taxa, to an areal flux rate based on laboratory measurements of metabolic excretion of two abundant species suggested that excretion by ben-thic invertebrates is at least as important as any of the other identified processes for internal loading to the water column.

TMDL, Upper Klamath Lake
2015Susan A. Wherry, Tamara M. Wood, Chauncey W. AndersonRevision and Proposed Modification of a Total Maximum Daily Load Model for Upper Klamath Lake, Oregon18010206

This report presents Phase 2 of the review and development of the mass balance water-quality model, originally developed in 2001, that guided establishment of the phosphorus (P) total maximum daily load (TMDL) for Upper Klamath and Agency Lakes, Oregon. The purpose of Phase 2 was to incorporate a longer (19-year) set of external phosphorus loading data into the lake TMDL model than had originally been available, and to develop a proof-of-concept method for modeling algal mortality and the consequent decrease in chlorophyll a that had not been possible with the 2001 TMDL model formulation.

Using the extended 1991–2010 external phosphorus loading dataset, the lake TMDL model was recalibrated following the same procedures outlined in the Phase 1 review. The version of the model selected for further development incorporated an updated sediment initial condition, a numerical solution method for the chlorophyll a model, changes to light and phosphorus factors limiting algal growth, and a new pH-model regression, which removed Julian day dependence in order to avoid discontinuities in pH at year boundaries. This updated lake TMDL model was recalibrated using the extended dataset in order to compare calibration parameters to those obtained from a calibration with the original 7.5-year dataset. The resulting algal settling velocity calibrated from the extended dataset was more than twice the value calibrated with the original dataset, and, because the calibrated values of algal settling velocity and recycle rate are related (more rapid settling required more rapid recycling), the recycling rate also was larger than that determined with the original dataset. These changes in calibration parameters highlight the uncertainty in critical rates in the Upper Klamath Lake TMDL model and argue for their direct measurement in future data collection to increase confidence in the model predictions.

TMDL, Upper Klamath Lake
2012William W. Walker, Jeffrey D. Walker, Jacob Kann,Evaluation of Water and Nutrient Balances for the Upper Klamath Lake Basin in Water Years 1992-2010.18010206

Upper Klamath and Agency Lakes (UKL) comprise a large, shallow, hypereutrophic lake system located in south-central Oregon that is seasonally dominated by large blooms of the nitrogen-fixing cyanobacterium Aphanizomenon flos-aquae. Bloom-driven water quality degradation that includes extended periods of low dissolved oxygen, elevated pH, and toxic levels of un-ionized ammonia has been associated with the decline of native endangered fish populations, including the Federally Listed shortnose (Chasmistes brevirostris) and Lost River (Deltistes luxatus) suckers. More specifically these conditions have been linked to large die-offs and redistribution of the endangered sucker species in UKL. Several studies have documented that recurring algal blooms and their decline are associated with periods of elevated pH, toxic levels of un-ionized ammonia, and depressed dissolved oxygen concentrations. Based on exceedances of water quality standards for dissolved oxygen, pH, and chlorophyll (algal biomass), both lakes were designated as water quality limited for resident fish and aquatic life.

Nutrient Balances, TMDL, Lake Dynamics,
2016Reclamation (Bureau of Reclamation)SECURE Water Act Section 9503(c)— Reclamation Climate Change and Water 2016, , , 180102

Chapter 5: Klamath River Basin. This summary chapter is part of the 2016 SECURE Water Act Report to Congress prepared by the Bureau of Reclamation (Reclamation) in accordance with Section 9503 of the SECURE Water Act. The 2016 SECURE Water Act Report follows and builds on the first SECURE Water Act Report, submitted to Congress in 2011,1 which characterized the impacts of warmer temperatures, changes to precipitation and snowpack, and changes to the timing and quantity of streamflow runoff across the West. This chapter provides a basin-specific summary for the Klamath River Basin.

The key study referred to in this chapter is the Klamath River Basin Study, which is being conducted through a partnership between Reclamation, Oregon’s Water Resources Department, and California’s Department of Water Resources to identify strategies to address current and future water demands in the basin. The Klamath River Basin Study is anticipated to be available in 2016. Because the Klamath River Basin Study is not yet complete, portions of this chapter are limited to a description of ongoing activities rather than final results. Additional information relevant to the Klamath River Basin, including the latest climate and hydrology projections for the basin, is included in Chapter 2: Hydrology and Climate Assessment.

Climate Change, Trinity Dam, Lewiston Dam, Clear Lake Dam, Gerber Dam, Link River Dam, Resource management,
2013William T. Peterson, Cheryl A. Morgan, Jay O. Peterson, Jennifer L. Fisher, Brian J. Burke, Kurt FreshOcean Ecosystem Indicators of Salmon Marine Survival in the Northern California Current,

As many scientists and salmon managers have noted, variations in marine survival of salmon often correspond with periods of alternating cold and warm ocean conditions. For example, cold conditions are generally good for Chinook (Oncorhynchus tshawytscha) and coho (O. kisutch) salmon, whereas warm conditions are not. These pages are based on our annual report of how physical and biological ocean conditions may affect the growth and survival of juvenile salmon in the northern California Current off Oregon and Washington. We present a number of physical, biological, and ecosystem indicators to specifically define the term "ocean conditions." More importantly, these metrics can be used to forecast the survival of salmon 1–2 years in advance. This information is presented for the non–specialist; additional detail is provided via links when possible.

Chinook Salmon, Coho Salmon, Ocean Ecosystem Indicators, Biological indicators,
2000David L. Perkins, Jacob Kann, G. Gary ScoppettoneThe Role of Poor Water Quality and Fish Kills in the Decline of Endangered Lost River and Shortnose Suckers in Upper Klamath Lake, , , , 18010206

Lost River (Deltistes luxatus) and shortnose (Chasmistes brevirostris) suckers are federally endangered species endemic to shallow lakes of the Upper Klamath River Basin in Oregon and California. Upper Klamath Lake represents the majority of the remaining habitat of these suckers, but has been a site of intermittent fish kills. We studied fish kills and associated water quality dynamics in the lake in 1995, 1996, and 1997 to determine factors responsible for dieoffs. Over 7,000 dead suckers were collected in the three years, and 85% of annual collections occurred during a 15-20 day period that began between mid August and late September. Suckers collected during the fish kills, as well as live fish captured the following spring, had a high incidence of afflictions such as parasitic and bacterial infections, cysts, and ulcers. The 1995 and 1996 fish kills were biased toward larger species (suckers), and larger individuals within species. Water quality in the lake was largely influenced by the dynamics of the bluegreen algae Aphanizomenon flos-aquae, which comprised over 90% of algal biomass. Associated with each fish kill was an extended period of water column stability and high algal biomass (>150 μg L-1 chlorophyll a) before the kills, followed by a well-mixed water column and algal collapse with little residual algae. Before the kills, algal photosynthesis caused high pH (9-10) for 30-90 days, which maintained a large proportion of the total ammonia in the toxic, unionized form (200-2000 μg L-1 NH3). Algal collapse decreased photosynthesis and increased biological oxygen demand, leading to dissolved oxygen levels less than 4.0 mg/l throughout the water column for 10-24 hours a day, for up to several days. Fish mortality coincided with algal bloom collapse and continued for 20-30 days after the period of low dissolved oxygen. We concluded that hypoxia, caused by the collapse of A. flos-aquae blooms, was the primary mechanism that triggered the 1995-97 fish kills.

Suckers, Water temperature, Disease, Fish Kills, Water quality,
2017State of Oregon of Environmental QualityUpper Klamath and Lost River Subbasins TMDL Chapter 2: Klamath River Dissolved Oxygen, Chlorophyll a, pH, and Ammonia Toxicity, , , , , , 18010206

The Upper Klamath Subbasin and Lost River Subbasin Total Maximum Daily Loads (TMDLs) and Water Quality Implementation Plan (WQMP) establish water quality goals for waterbodies in these two subbasins which are within the Klamath Basin. The WQMP lays out steps toward meeting these goals. Water quality improvement programs that lead to TMDL attainment will advance Oregon's commitment to protecting beneficial uses in compliance with State and Federal Law. To accomplish this, the State has promoted a path that progresses towards water quality standard compliance, with protection of the beneficial uses of waters of the State as the primary goal. It is anticipated that facilities, sectors and management agencies will utilize this TMDL to develop and/or alter water quality management efforts. In addition, this TMDL should be used to track water quality, instream physical parameters and landscape conditions through time. This report presents the Upper Klamath and Lost River Subbasins TMDL. It addresses the elements of a TMDL required by the U.S. Environmental Protection Agency (EPA). These elements include:
• A description of the geographic area to which the TMDL applies;
• Specification of the applicable water quality standards;
• An assessment of the problem, including the extent of deviation of ambient conditions from water quality
standards;
• The development of a loading capacity including those based on surrogate measures and including flow
assumptions used in developing the TMDL;
• Identification of point sources and nonpoint sources; development of Waste Load Allocations for point
sources and Load Allocations for nonpoint sources;
• Development of a margin of safety; and
• An evaluation of seasonal variation.

Total Maximum Daily Loads (TMDLs), Upper Klamath, Lost River, Water quality,
2013National Marine Fisheries Service, U.S. Fish and Wildlife ServiceBiological Opinions on the Effects of Proposed Klamath Project Operations from May 31, 2013, through March 31, 2023, on Five Federally Listed Threatened and Endangered Species, , , 180102

The Klamath Basin’s hydrologic system currently consists of a complex of interconnected rivers, canals, lakes, marshes, dams, diversions, wildlife refuges, and wilderness areas. Alterations to the natural hydrologic system began in the late 1800s and expanded in the early 1900s, including water diversions by private water users, Reclamation’s Project, and several hydroelectric dams operated by a private company, currently known as PacifiCorp. PacifiCorp’s Klamath Hydroelectric Project (KHP) was constructed between 1911 and 1962, and includes eight developments: (1) East and (2) West Side power facilities at Link River Dam; (3) Keno Dam; (4) J.C. Boyle Dam; (5) Copco 1 Dam; (6) Copco 2 Dam; (7) Fall Creek Dam; and (8) Iron Gate Dam (IGD). The Link River Dam and Upper Klamath Lake (UKL) are not part of the KHP. PacifiCorp operated the KHP under a 50-year license issued by the Federal Energy Regulatory Commission (FERC) until the license expired in 2006. PacifiCorp continues to operate the KHP under annual licenses based on the terms of the previous license. In 2001, the Services issued BiOps on the effects of Reclamation’s Project operations on listed species, and concluded that the proposed Project operations would likely jeopardize the continued existence of the Lost River sucker (LRS) and the shortnose sucker (SNS) in UKL (USFWS 2001) and the Southern Oregon/Northern California Coast (SONCC) coho salmon Evolutionarily Significant Unit (ESU) (NMFS 2001a). Because of a severe drought in 2001 and the jeopardy BiOps, Reclamation limited the volume of water delivered to Project agricultural users, and to the Lower Klamath and Tule Lake National Wildlife Refuges.

Shortnose sucker, Lost River sucker, Green sturgeon, Coho Salmon, Eulachon, Conservation, Critical Habitat
2008Katharine Carter, Steve Kirk, North Coast Regional Water Quality Control BoardAppendix 5 Fish and Fishery Resources of the Klamath River Basin, , 180102

The Klamath River basin contains 83 species of fish, 45 of which are native to the Klamath drainage and 38 that have been introduced and are non-native. Fourteen of the native fish species in the basin have been granted special federal and/or state status. The following discussion of fish species and resources in the basin is divided into three parts: fish species found above Iron Gate Dam in California and Oregon, fish species found from Iron Gate Dam to the Ocean in California, and Chinook, steelhead, and coho salmonids from Iron Gate Dam to the Ocean in California.

North Coast Regional Water Quality Control Board, Fall Chinook Salmon, Steelhead Trout, Spring Chinook Salmon, Coho Salmon, Iron Gate Dam
2009Kathryn KostowFactors that contribute to the ecological risks of salmon and steelhead hatchery programs and some mitigating strategies,

State and federal agencies in the United States annually release millions of hatchery salmon and steelhead into public waters. Many of the hatchery programs are located in areas where the wild populations are now listed under the U.S. Endangered Species Act (ESA) (16 U.S.C. §§ 1531–1544). These hatchery programs pose genetic and ecological risks to wild fish populations. Genetic risks occur when hatchery and wild fish interbreed and usually occur within a taxonomic species. Ecological risks occur when the presence of hatchery fish affects how wild fish interact with their environment or with other species and may affect whole species assemblages. This paper reviews some of the factors that contribute to ecological risks. Important contributing factors include the relative abundance of hatchery and wild fish in natural production areas, hatchery programs that increase density-dependant mortality, residual hatchery fish, some physical advantages that hatchery fish can have over wild fish, and life history characteristics that may make some species especially vulnerable to the effects of ecological risks. Many of these risk factors can be mitigated by management activities that reduce the level of interactions between hatchery and wild fish. This paper concludes by recommending twelve mitigation strategies that may be useful when agencies need to bring hatchery programs into compliance with the take provisions of the ESA.

Salmon, Steelhead, Hatchery, Ecology, Risk
2004J.M. Eilers, J. Kann, J. Cornett, K.Moser, St.AmandPaleolimnological evidence of change in a shallow, hypereutrophic lake: Upper Klamath Lake, Oregon, USA, , 18010206

Sediment cores were collected from Upper Klamath Lake in October, 1998 and analyzed for 210Pb, 14C, 15N, N, P, C, Ti, Al, diatoms, Pediastrum, and cyanobacterial akinetes. These results were used to reconstruct changes in water quality in Upper Klamath Lake over the last 150 years. The results showed that there was substantial mixing of the upper 10 cm of sediment, representing the previous 20 to 30 years. However, below that, 210Pb activity declined monotonically, allowing reasonable dating for the period from about 1850 to 1970. The sediment accumulation rates (SAR) showed a substantial increase in the 20th century. The increase in SAR corresponded with increases in erosional input from the watershed as represented by the increases in sediment concentrations of Ti and Al. The upper 20 cm of sediment, representing the last 150 years, also showed increases in C, N, P, and 15N. The increases in nutrient concentrations may be affected to various degrees by diagenetic reactions within the sediments, although the changes in concentrations also were marked by changes in the N:P ratio and in a qualitative change in the source of N as reflected in increasing δ15N. The diatoms showed modest changes in the 20th century, with increases in Asterionella formosa, Stephanodiscus hantzschii, and S. parvus. Pediastrum, a green alga, was well-preserved in the sediments and exhibited a sharp decline in relative abundance in the upper sediments. Total cyanobacteria, as represented by preserved akinetes, exhibited only minor changes in the last 1000 years. However, Aphanizomenon flos-aquae, a taxon which was formerly not present in the lake 150 years ago, but that now dominates the summer phytoplankton, has shown major increases over the past 100 years. The changes in sediment composition are consistent with activities including timber harvest, drainage of wetlands, and agricultural activities associated with livestock grazing, irrigated cropland, and hydrologic modifications.

Paleolimnology, Aphanizomenon flos-aquae, akinetes, Upper Klamath Lake
2008Stephen R. CarpenterPhosphorus control is critical to mitigating eutrophication

The Midwest floods of 2008 added more than just water to the region’s lakes, reservoirs, and rivers. Runoff from farms and towns carries a heavy load of silt, nutrients, and other pollutants. The nutrients trigger blooms of algae, which taint drinking water. Death and decay of the algae depletes oxygen, kills fish and bottom-dwelling animals, and thereby creates ‘‘dead zones’’ in the body of water. The syndrome of excessive nutrients,
noxious algae, foul water, and dead zones—which ecologists call eutrophication— is depressingly familiar to those who depend on water from rich agricultural regions.

The cure sounds simple: decrease inputs of nutrients, especially nitrogen (N) and phosphorus (P). But which nutrient,
and how deeply should the inputs be cut? In this issue of PNAS, Schindler et al. (1) present a remarkable 37-year experiment on nutrient management in Canadian lakes which shows that P inputs directly control algae blooms. Surprisingly, however, the authors also observed that algae blooms are made worse if N inputs are decreased without also decreasing P inputs. This finding is of critical importance for current programs aimed at mitigating eutrophication of both freshwaters and coastal oceans.

Human activity has greatly increased the inputs of reactive N and P to the biosphere. Reactive N (biologically active forms such as nitrate, ammonia, or organic N compounds, in contrast to N2 gas, which is not used by organisms except for a few nitrogen-fixing species) is supplied by natural sources, as well as by human activities such as industrial N2 fixation, combustion, and planting of soybeans and other N2-fixing crops. Global flux of reactive N to the biosphere from food production has increased from 15 Tg N year1 in 1860 to 187 Tg N year1 in 2005 (2). Additional reactive N is fixed for industrial or household use or is inadvertently created as a byproduct of fossil fuel combustion. Excess reactive N enters groundwater, surface water, or the atmosphere.

Water quality, Eutrophication
2009By Kurt D. Carpenter, Daniel T. Snyder, John H. Duff, Frank J. Triska, Karl K. Lee, Ronald J. Avanzino, Steven SobieszczykHydrologic and Water-Quality Conditions During Restoration of the Wood River Wetland, Upper Klamath River Basin, Oregon, 2003–05, , 18010206

Restoring previously drained wetlands is a strategy currently being used to improve water quality and decrease nutrient loading into Upper Klamath Lake, Oregon. In this 2003–05 study, ground- and surface-water quality and hydrologic conditions were characterized in the Wood River Wetland. Nitrogen and phosphorus levels, primarily as dissolved organic nitrogen and ammonium (NH4) and soluble reactive phosphorus (SRP), were high in surface waters. Dissolved organic carbon concentrations also were elevated in surface water, with median concentrations of 44 and 99 milligrams of carbon per liter (mg-C/L) in the North and South Units of the Wood River Wetland, respectively, reaching a maximum of 270 mg-C/L in the South Unit in late autumn. Artesian well water produced NH4 and SRP concentrations of about 6,000 micrograms per liter (μg/L), and concentrations of 36,500 μg-N/L NH4 and 4,110 μg-P/L SRP in one 26–28 ft deep piezometer well. Despite the high ammonium concentrations, the nitrate levels were moderate to low in wetland surface and ground waters. The surface-water concentrations of NH4 and SRP increased in spring and summer, outpacing those for chloride (a conservative tracer), indicative of evapoconcentration. In-situ chamber experiments conducted in June and August 2005 indicated a positive flux of NH4 and SRP from the wetland sediments. Potential sources of NH4 and SRP include diffusion of nutrients from decomposed peat, decomposing aquatic vegetation, or upwelling ground water. In addition to these inputs, evapoconcentration raised surface-water solute concentrations to exceedingly high values by the end of summer. The increase was most pronounced in the South Unit, where specific conductance reached 2,500 μS/cm and median concentrations of total nitrogen and total phosphorus reached 18,000–36,500 μg-N/L and about 18,000–26,000 μg-P/L, respectively.

Hydrologic conditions, Water quality, Upper Klamath
2003Mike Turaski, The Bureau of Land Management (BLM)2002 and 2003 Upper Klamath River Water Temperature Monitoring, 18010206

The Bureau of Land Management (BLM) conducted water temperature monitoring at various sites in the Klamath River in 2003 and 2003. The objectives of this effort were to (1) characterize spatial and seasonal trends water temperature trends in the Upper Klamath Wild and Scenic River and adjacent river reaches and (2) provide high quality water temperature data for use by stakeholders in the ongoing FERC relicensing and TMDL processes.

In addition to summaries of the water temperature data, two other data sets are presented in this report. Instantaneous (collected every 30 minutes) and average daily streamflow is monitored by the USGS, and is provided herein to provide context for interpreting water temperature trends. Air temperature was monitored by the BLM at the USGS stream gauge. This data also helps explain observed water temperatures.

Water Temperature, Air Temperature, The Bureau of Land Management (BLM), Upper Klamath
2015Damon H. Goodman, Nicholas A. Som, Justin Alvarez, Aaron MartinA mapping technique to evaluate age-0 salmon habitat response from restoration, , 18010209

To combat decades of anthropogenic degradation, restoration programs seek to improve ecological conditions through habitat enhancement. Rapid assessments of condition are needed to support adaptive management programs and improve the understanding of restoration effects at a range of spatial and temporal scales. Previous attempts to evaluate restoration practices on large river systems have been hampered by assessment tools that are irreproducible or metrics without clear connections to population responses. We modified a demonstration flow assessment approach to assess the realized changes in habitat quantity and quality attributable to restoration effects.We evaluated the technique’s ability to predict anadromous salmonid habitat and survey reproducibility on the Trinity River in northern California. Fish preference clearly aligned with a priori designations of habitat quality: the odds of observing rearing Chinook or coho salmon within high-quality habitats ranged between 10 and 16 times greater than low qualities, and in all cases the highest counts were associated with highest quality habitat. In addition, the technique proved to be reproducible with “substantial” to “almost perfect” agreement of results from independent crews, a considerable improvement over a previous demonstration flow assessment. These results support the use of the technique for assessing changes in habitat from restoration efforts and for informing adaptive management decisions.

Demonstration Flow Assessment, Habitat Modeling, Habitat Validation, Restoration Effectiveness Monitoring
2015Megan Rocha, Karuk Department of Natural ResourcesKaruk Department of Natural Resources Strategic Plan for Organizational Development, , , 18010209

The Karuk Department of Natural Resources has completed a strategic planning process to address organizational needs focused on staffing capacity and infrastructure. This planning process has involved all management-level staff within the Department to ensure all program area needs can be adequately addressed and the expertise of staff could be leveraged. DNR has grown tremendously since inception in 1989, from a single employee to a department that has exceeded a hundred (100) employees during wildland fire events. This plan provides a strategy-based approach to reorganize the existing capacity in a manner that enhances efficiencies and opportunities for synergy. This includes structural reorganization at both programmatic and staffing levels. The outcome is three (3) Branches within the Department: a) Administrative Operations and Development; b) Eco-Cultural Revitalization; and c) Watersheds, as well as Programs within each that can address identified programmatic and functional areas. Moreover, this plan provides a clear path for projected growth and development based on identified needs and opportunities, both for staffing and infrastructure. Infrastructure needs and growth at a centralized location in Orleans has been developed into a Master Site Plan, preliminary design renderings, a cost estimate that can be used to pursue facilities funding development. With this plan, the Karuk Department of Natural Resources has taken a proactive and inclusive approach to develop a strategy-based plan for the next five (5) years that will allow for the Mission of the Department to be met in a more comprehensive manner.

Strategic Plan, Action Plan, Evaluation Plan, Karuk Tribal Council, Air Quality, Cultural Resources, Enforcement/Regulation, Environmental Education, Environmental Justice, Fisheries, Watershed Restoration, Water Quality
2013Dana E. Weigel, Patrick J. Connolly, Madison S. PowellThe impact of small irrigation diversion dams on the recent migration rates of steelhead and redband trout (Oncorhynchus mykiss),

Barriers to migration are numerous in stream environments and can occur from anthropogenic activities (such as dams and culverts) or natural processes (such as log jams or dams constructed by beaver (Castor canadensis)). Identification of barriers can be difficult when obstructions are temporary or incomplete providing passage periodically. We examine the effect of several small irrigation diversion dams on the recent migration rates of steelhead (Oncorhynchus mykiss) in three tributaries to the Methow River, Washington. The three basins had different recent migration patterns: Beaver Creek did not have any recent migration between sites, Libby Creek had two-way migration between sites and Gold Creek had downstream migration between sites. Sites with migration were significantly different from sites without migration in distance, number of obstructions, obstruction height to depth ratio and maximum stream gradient. When comparing the sites without migration in Beaver Creek to the sites with migration in Libby and Gold creeks, the number of obstructions was the only significant variable. Multinomial logistic regression identified obstruction height to depth ratio and maximum stream gradient as the best fitting
model to predict the level of migration among sites. Small irrigation diversion dams were limiting population interactions in Beaver Creek and collectively blocking steelhead migration into the stream. Variables related to stream resistance (gradient, obstruction number and obstruction height to depth ratio) were better predictors of recent migration rates than distance, and can provide important insight into migration and population demographic processes in lotic species.

Migration, Isolation by resistance, Isolation by distance, Landscape genetics, Steelhead
2015Jonathan A. Warrick, Jennifer A. Bountry, Amy E. East, Christopher S. Magirl, Timothy J. Randle, Guy Gelfenbaum, Andrew C. Ritchie, George R. Pess Vivian Leung, Jeffrey J. DudaLarge-scale dam removal on the Elwha River, Washington, USA: Source-to-sink sediment budget and synthesis

Understanding landscape responses to sediment supply changes constitutes a fundamental part of many problems in geomorphology, but opportunities to study such processes at field scales are rare. The phased removal of two large dams on the Elwha River, Washington, exposed 21 ± 3 million m3, or ~30 million tonnes (t), of sediment that had been deposited in the two former reservoirs, allowing a comprehensive investigation of watershed and coastal responses to a substantial increase in sediment supply. Here we provide a source-to-sink sediment budget of this sediment release during the first two years of the project (September 2011–September 2013) and synthesize the geomorphic changes that occurred to downstream fluvial and coastal landforms. Owing to the phased removal of each dam, the release of sediment to the river was a function of the amount of dam structure removed, the progradation of reservoir delta sediments, exposure of more cohesive lakebed sediment, and the hydrologic conditions of the river. The greatest downstream geomorphic effects were observed after water bodies of both reservoirs were fully drained and fine (silt and clay) and coarse (sand and gravel) sediments were spilling past the former dam sites. After both dams were spilling fine and coarse sediments, river suspended-sediment concentrations were commonly several thousand mg/L with ~50% sand during moderate and high river flow. At the same time, a sand and gravel sediment wave dispersed down the river channel, filling channel pools and floodplain channels, aggrading much of the river channel by ~1 m, reducing river channel sediment grain sizes by ~16-fold, and depositing ~2.2million m3 of sand and gravel on the seafloor offshore of the rivermouth.

Dam removal, Sediment budget, River restoration, Elwha River, Sediment wave
2015Christopher M. Tonra, Kimberly Sager-Fradkin, Sarah A. Morley, Jeffrey J. Duda, Peter P. MarraThe rapid return of marine-derived nutrients to a freshwater food web following dam removal

Damremoval is increasingly being recognized as a viable river restoration action. Although themain beneficiaries of restored connectivity are often migratory fish populations, little is known regarding recovery of other parts of the freshwater foodweb, particularly terrestrial components.Wemeasured stable isotopes in key components to the freshwater food web: salmon, freshwater macroinvertebrates and a river specialist bird, American dipper (Cinclus mexicanus), before and after removal of the Elwha Dam,WA, USA. Less than a year after dam removal, salmon returned to the systemand released marine-derived nutrients (MDN). In that same yearwe documented an increase in stable-nitrogen and carbon isotope ratios in American dippers. These results indicate that MDN from anadromous fish, an important nutrient subsidy that crosses the aquatic–terrestrial boundary, can return rapidly to food webs after dams are removed which is an important component of ecosystem recovery.

American dipper, Cinclus mexicanus, Elwha River, Salmon, Stable isotopes, Oncorhynchus spp.
2016K. F. Tiffan, J. R. Hatten, D. A. TrachtenbargAssessing Juvenile Salmon Rearing Habitat and Associated Predation Risk in a Lower Snake River Reservoir

Subyearling fall Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River basin exhibit a transient rearing strategy and depend on connected shoreline habitats during freshwater rearing. Impoundment has greatly reduced the amount of shallow-water rearing habitat that is exacerbated by the steep topography of reservoirs. Periodic dredging creates opportunities to strategically place spoils to increase the amount of shallow-water habitat for subyearlings while at the same time reducing the amount of unsuitable area that is often preferred by predators. We assessed the amount and spatial arrangement of subyearling rearing habitat in Lower Granite Reservoir on the Snake River to guide future habitat improvement efforts. A spatially explicit habitat assessment was conducted using physical habitat data, two-dimensional hydrodynamic modelling and a statistical habitat model in a geographic information system framework. We used field collections of subyearlings and a common predator [smallmouth bass (Micropterus dolomieu)] to draw inferences about predation risk within specific habitat types. Most of the high-probability rearing habitat was located in the upper half of the reservoir where gently sloping landforms created low lateral bed slopes and shallow-water habitats. Only 29% of shorelines were predicted to be suitable (probability >0.5) for subyearlings, and the occurrence of these shorelines decreased in a downstream direction. The remaining, less suitable areas were composed of low-probability habitats in unmodified (25%) and riprapped shorelines (46%). As expected, most subyearlings were found in high-probability habitat, while most smallmouth bass were found in low-probability locations. However, some subyearlings were found in low-probability habitats, such as riprap, where predation risk could be high. Given their transient rearing strategy and dependence on shoreline habitats, subyearlings could benefit from habitat creation efforts in the lower reservoir

Habitat, Fall Chinook Salmon, Smallmouth bass, Snake River, Modelling, Predation, Riprap, Lower Granite Reservoir
2014G. R. Pess, T. P. Quinn, S. R. Gephard, R. SaundersRe-colonization of Atlantic and Pacific rivers by anadromous fishes: linkages between life history and the benefits of barrier removal, ,

The last two decades have seen a rapid increase in barrier removals on rivers of the Northern Hemisphere, often for the explicit purpose of expanding the abundance, spatial distribution, and life history diversity of migratory fishes. However, differences in life history such as seasonal timing of migration and reproduction, iteroparity versus semelparity, and the extent of natal homing are likely to affect the capacity
for expansion and re-colonization by taxa such as alosines, lamprey, and salmonids. We first review some basic life history traits that may affect re-colonization by migratory fishes, and then present selected examples from Atlantic and Pacific basins to illustrate these patterns and their implications for the success of barrier removal as a measure to advance the goal of fish conservation.We conclude that diadromous fishes have
the capacity to rapidly re-colonize newly available habitats, though the life history patterns of each species, the proximity to source populations in the same or nearby river systems, and the diversity of habitats available may control the patterns and rates of recolonization.

Anadromous, Life history, Dam removal, Conservation, Homing, Restoration
2016J. R. Hatten, T. R. Batt, J. J. Skalicky, R. Engle, G. J. Barton, R. L. Fosness, J. WarrenEffects of dam removal on Tule Fall Chinook Salmon spawning habitat in the White Salmon river, Washington, , ,

Condit Dam is one of the largest hydroelectric dams ever removed in the USA. Breached in a single explosive event in October 2011, hundreds-of-thousands of cubic metres of sediment washed down the White Salmon River onto spawning grounds of a threatened species, Columbia River tule fall Chinook salmon Oncorhynchus tshawytscha. We investigated over a 3-year period (2010–2012) how dam breaching affected channel morphology, river hydraulics, sediment composition and tule fall Chinook salmon (hereafter ‘tule salmon’) spawning habitat in the lower 1.7 km of the White Salmon River (project area). As expected, dam breaching dramatically affected channel morphology and spawning habitat due to a large load of sediment released from Northwestern Lake. Forty-two per cent of the project area that was previously covered in water was converted into islands or new shoreline, while a large pool near the mouth filled with sediments and a delta formed at the mouth. A two-dimensional hydrodynamic model revealed that pool area decreased 68.7% in the project area, while glides and riffles increased 659% and 530%, respectively. A spatially explicit habitat model found the mean probability of spawning habitat increased 46.2% after dam breaching due to an increase in glides and riffles. Shifting channels and bank instability continue to negatively affect some spawning habitat as sediments continue to wash downstream from former Northwestern Lake, but 300m of new spawning habitat (river kilometre 0.6 to 0.9) that formed immediately postbreach has persisted into 2015. Less than 10% of tule salmon have spawned upstream of the former dam site to date, but the run sizes appear healthy and stable. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

fall run chinook, dam removal, spawning habitat
2013Karl D. Burton , Larry G. Lowe , Hans B. Berge , Heidy K. Barnett, Paul L. FauldsComparative Dispersal Patterns for Recolonizing Cedar River Chinook Salmon above Landsburg Dam, Washington, and the Source Population below the Dam

Anadromous salmonid populations are particularly vulnerable tomigration blockages, such as dams and culverts, because access to historic spawning and rearing habitats is prevented. The process of salmonid recolonization has not been well documented for river systems where anthropogenic migration barriers have been removed or where fish passage facilities have been constructed. In September 2003, Seattle Public Utilities completed construction of a fish passage facility that circumvented Landsburg Dam on the Cedar River,Washington. Chinook Salmon Oncorhynchus tshawytscha spawned in newly availablemain-stem habitats immediately after fish passage facility construction and in all subsequent years. Further dispersal into tributary habitats occurred 5 years after construction. Redds tended to be concentrated in the downstream third of the available habitat above the dam, although some fish did utilize suitable spawning sites throughout the main stem, even in the uppermost reaches of the newly available habitat. Median spawn timing for redds observed above the dam was not significantly different from spawn timing for the source population, indicating that migration delays through the fish passage facility were minimal. Male Chinook Salmon consistently outnumbered females, with annual sex ratios ranging from 1.3:1 to 4.7:1. Chinook Salmon spawning above the dam contributed between 2.7% and 14.7% of the total annual redd count (2003–2010) for Cedar River Chinook Salmon; upstream redds as a percentage of total redds increased over time, indicating that a new, naturally reproducing population above the dam was growing. The proportion of hatchery-origin fish spawning above the dam decreased over the duration of the study but was consistently higher than the hatchery component observed below the dam.

Chinook Salmon, Recolonization, Redd Abundance
2014Joseph H. Anderson, Paul L. Faulds, Karl D. Burton, Michele E. Koehler, William I. Atlas, Thomas P. QuinnDispersal and productivity of Chinook (Oncorhynchus tshawytscha) and coho (Oncorhynchus kisutch) salmon colonizing newly accessible habitat, ,

Following construction of a fish ladder at Landsburg Diversion Dam on the Cedar River, Washington, USA, in fall 2003, we used DNA-based parentage to identify second generation Chinook (Oncorhynchus tshawytscha) and coho (Oncorhynchus kisutch) salmon as recruits that were produced above the dam or “strays” dispersing into the new habitat that were produced elsewhere. For both species, strays colonized immediately but decreased as a proportion of the total run over time. Chinook salmon strays were more numerous in years when the species was more abundant below the dam and included a much larger proportion of hatchery origin salmon than did coho salmon. Productivity, calculated as the ratio of female recruits sampled at the dam to female spawners, exceeded replacement in all four coho salmon cohorts but only two of five Chinook salmon cohorts, leading to more rapid population expansion of coho salmon. However, estimates of fishing mortality and recruitment into the Cedar River below the dam substantially increased Chinook salmon productivity estimates. Our results demonstrate that Pacific salmon are capable of rapidly recolonizing habitat made accessible by restoration and emphasize the importance of demographic exchange with preexisting populations during the transition from recolonization to self-sustainability.

Coho Salmon, Chinook Salmon, Recolonizing Habitat
2014Joseph H. Anderson, George R. Pess, Richard W. Carmichael, Michael J. Ford, Thomas D. Cooney, Casey M. Baldwin, Michelle M. McClurePlanning Pacific Salmon and Steelhead Reintroductions Aimed at Long-Term Viability and Recovery,

Local extirpations of Pacific salmon Oncorhynchus spp. and steelhead O. mykiss, often due to dams and other stream barriers, are common throughout the western United States. Reestablishing salmonid populations in areas they historically occupied has substantial potential to assist conservation efforts, but best practices for reintroduction are not well established. In this paper, we present a framework for planning reintroductions designed to promote the recovery of salmonids listed under the Endangered Species Act. Before implementing a plan, managers should first describe the benefits, risks, and constraints of a proposed reintroduction.We define benefits as specific biological improvements towards recovery objectives. Risks are the potential negative outcomes of reintroductions that could worsen conservation status rather than improve it. Constraints are biological factors that will determine whether the reintroduction successfully establishes a self-sustaining population.We provide guidance for selecting a recolonization strategy (natural colonization, transplanting, or hatchery releases), a source population, and a method for providing passage that will maximize the probability of conservation benefit while minimizing risks. Monitoring is necessary to determine whether the reintroduction successfully achieved the benefits and to evaluate the impacts on nontarget species or populations. Many of the benefits, especially diversity and the evolution of locally adapted population
segments, are likely to accrue over decadal time scales. Thus, we view reintroduction as a long-term approach to enhancing viability. Finally, our review of published salmonid reintroduction case studies suggests that large uncertainties remain in the success of reintroduction in establishing self-sustaining populations, particularly for programs employing active methods.

Long-Term Viability, Reintroductions, Salmon, Steelhead
2013ReclamationEnvironmental Assessment. 2013 Lower Klamath River Late-Summer Flow Augmentation from Lewiston Dam18010209

In August and September 2002, an estimated 170,000 fall-run Chinook salmon returned to the Klamath River, and a substantial number of adult Chinook salmon and other salmonids died prematurely in the lower Klamath River. This included an estimated 344 coho salmon listed as threatened under the Endangered Species Act (ESA). Federal, tribal, and state biologists studying the die-off concluded that: (1) pathogens Ichthyophthirius multifiliis (Ich) and Flavobacterium columnare (Columnaris) were the primary causes of death to fish; and (2) warm water temperatures, low water velocities and volumes, high fish density, and long fish residence times likely contributed to the disease outbreaks and subsequent mortalities (Guillen 2003; Belchik et al. 2004; Turek et al. 2004). Flows in the lower Klamath averaged about 2,000 cubic feet per second (cfs) during September 2002.

In 2003, 2004, and 2012, predictions of large runs of fall-run Chinook salmon to the Klamath River Basin and drier than normal hydrologic conditions prompted Reclamation to arrange for late-summer flow augmentation to increase water volumes and velocities in the lower Klamath River to reduce the probability of a disease outbreak in those years. Thirty-eight thousand acre-feet (TAF) of supplemental water was released from Trinity Reservoir in 2003, and 36 TAF in 2004, and 39 TAF in 2012. While documentation of the effectiveness of these events is limited, general observations were that implementation of the sustained higher releases from August to early September in each year coincided with no significant disease or adult mortalities.

Environmental Assessment, Flow Augmentation, Lewiston Dam
2015ReclamationEnvironmental Assessment. 2015 Lower Klamath River Late-Summer Flow Augmentation From Lewiston Dam18010209

This Environmental Assessment (EA) examines the potential direct, indirect, and cumulative impacts to the affected environment associated with the Bureau of Reclamation proposal to release supplemental flows from Lewiston Dam to improve water quality and reduce the prevalence of fish disease in the lower Klamath River. The Proposed Action will be implemented in late summer of 2015 to support the health of salmonid fish, including species that return to the Trinity River Basin to reproduce. The area of potential effect includes Trinity Reservoir and the Trinity River from Lewiston Dam to the confluence with the Klamath River, and the Klamath River to the Klamath River estuary near Klamath, California. Additionally, the affected environment includes the Sacramento River Basin as transbasin diversions from Trinity Reservoir via Lewiston Reservoir and the Clear Creek Tunnel to the Sacramento River Basin have occurred historically and are planned to occur throughout the summer (see Figure 1). This EA was prepared in accordance with the National Environmental Policy Act (NEPA), Council of Environmental Quality (CEQ) regulation (40 CFR Parts 1500-1508), and Department of the Interior Regulations (43 CFR Part 46).

Environmental Assessment, Flow Augmentation, Lewiston Dam
2005ReclamationNatural Flow of the Upper Klamath River, 18010203

This report presents details of the investigation and results in estimating the natural flow of the upper Klamath River at Keno, Oregon. The area investigated includes the Klamath River Basin above Keno, Oregon, primarily in Klamath County, with some areas of Siskiyou and Modoc Counties in California. The study area includes the Sprague, Williamson, and Wood River basins, as well as Upper Klamath and Lower Klamath Lakes.

The current purpose of this study is to provide an estimate of the monthly natural flows in the upper Klamath River at Keno. This estimate of the natural flow represents typical flow without agricultural development in the Upper Klamath River Basin, including its tributaries.

This study used a water budget approach to assess the agricultural depletions and alterations to the natural flow. The approach was to evaluate the changes of agriculture from predevelopment conditions, estimate the effects of these changes, and restore the water budget to natural conditions by reversing the effects of agricultural development. Records used in this empirical assessment were derived from both stream gaging flow histories and from climatological records for stations within and adjacent to the study area.

Natural flow,
2012U.S. Department of the Interior, California Department of Fish & GameKlamath Facilities Removal Final Environmental Impact Statement/Environmental Impact Report, , , 180102

This Klamath Facilities Removal Environmental Impact Statement/Environmental Impact Report (EIS/EIR) evaluates the potential impacts of the removal of the four PacifiCorp1 dams on the Klamath River as contemplated in the Klamath Hydroelectric Settlement Agreement (KHSA). The Klamath Basin Restoration Agreement (KBRA), as well as the transfer of Keno Dam, will be treated and analyzed as a connected action. Together, these two agreements attempt to resolve long-standing conflicts in the Klamath River Basin, located in southern Oregon and northern California. The KHSA and KBRA provide for the restoration of native fisheries and sustainable water supplies throughout the Klamath River Basin. Specifically, the KHSA established a process for a Secretarial Determination. This process includes studies, environmental review, and a decision by the Secretary of the Interior regarding whether removal of J.C. Boyle, Copco 1, Copco 2, and Iron Gate Dams (1) will advance restoration of salmonid (salmon, steelhead, and trout) fisheries of the Klamath Basin, and (2) is in the public interest, which includes but is not limited to, consideration of potential impacts on affected local communities and Tribes.

This EIS/EIR has been prepared according to requirements of the National Environmental Policy Act (NEPA) and the California Environmental Quality Act (CEQA). Direct, indirect, and cumulative impacts resulting from the project alternatives on the physical, natural, and socioeconomic environment of the region are addressed.

Environmental Impact Statement/Environmental Impact Report, Dam Removal, Salmon, Steelhead
2005North Coast Regional Water Quality Control Board, Donald A. CoatesStaff Report for the Action Plan for the Scott River Watershed. Sediment and Temperature Total Maximum Daily Loads, 18010209

This document is the Staff Report that supports and explains the Action Plan for the Scott River Watershed Sediment and Temperature Total Maximum Daily Loads (Scott River TMDL Action Plan). The Scott River TMDL Action Plan is proposed as an amendment to the Basin Plan. The Scott River watershed comprises approximately 520,184 acres (813 mi2) in Siskiyou County, California. The Scott River is tributary to the Klamath River.
Section 303(d) of the Clean Water Act requires states to compile a list of impaired water bodies that do not meet water quality standards. The Clean Water Act also requires states to establish total maximum daily loads (TMDLs) for such waters. The Scott River is listed under Section 303(d) as impaired by elevated sediment levels and elevated water temperatures. Adoption and approval of the Scott River TMDL Action Plan will establish the TMDLs and will satisfy the requirements of Section 303(d). The goal of the Scott River TMDL Action Plan is to achieve the TMDLs, achieve sediment and temperature water quality standards, and protect the beneficial uses of water in the Scott River watershed.

Water Temperature, Sediment, Total Maximum Daily Loads
2013CRS, Harold F. UptonCommercial Fishery Disaster Assistance,

Disaster relief may be provided by the federal government to assist the fishing industry when it is affected by a commercial fishery failure. A commercial fishery failure can be declared when fishermen endure economic hardships resulting from fish population declines or other disruptions to the fishery. The Department of Commerce can provide disaster assistance under Sections 308(b) and 308(d) of the Interjurisdictional Fisheries Act (16 U.S.C. §4107), as amended, and Sections 312(a) and 315 of the Magnuson-Stevens Fishery Conservation and Management Act (16 U.S.C §§1861a and 1864). The National Marine Fisheries Service plays a central role in determining whether a commercial fishery failure has occurred and in allocating federal funding to states and affected fishing communities. Congress plays a pivotal role by appropriating funds and providing oversight of the process. States also play a role by initiating requests, providing information, and planning for the use of funds. Oceanic conditions, climate, and weather events can impact fishery resources and/or commercial infrastructure such as boats, shoreside processing, and ports. Since 1994, federal commercial fishery failure determinations have been made on 42 occasions, and nearly $840 million in federal funding has been appropriated specifically for fishery disaster relief. Funds have been allocated to fisheries of the North Pacific, Pacific Northwest, Gulf of Mexico, and the East Coast. The most recent fishery failures have been declared for the Northeast multispecies fishery, Mississippi Sound fisheries, and certain Alaska Chinook salmon fisheries.

Commercial Fishery Disaster Assistance, Long-Term Management
2016Klamath Tribal Water Quality ConsortiumUpper Klamath Basin Nonpoint Source Pollution Assessment and Management Program Plan, , , , 18010203

The Consortium produced this Nonpoint Source (NPS) Assessment and Management Program Plan (AMPP) to address water quality issues in the Upper Klamath Basin which affect the Lower Klamath Basin (Figure 1). Water quality problems in the Upper Klamath Basin and its tributaries have been well documented in the Oregon Department of Environmental Quality Total Maximum Daily Loads (TMDLs) for Upper Klamath Lake (ODEQ 2002) and Upper Klamath and Lost rivers (ODEQ 2010b), California North Coast Regional Water Quality Control Board Klamath River TMDL (NCRWQCB 2010), evaluations of techniques for water quality improvement (Stillwater Sciences et al. 2012, 2013), an Environmental Impact Statement/Report for the proposed removal of the Klamath Hydroelectric Project (US DOI and CDFG 2012), and numerous other studies by federal, tribal, and state agencies. At Iron Gate Dam near the California border, the Klamath River water is often of insufficient quantity and poor quality to meet the needs of fish, wildlife, and humans. To address this problem, the Consortium’s goal is to improve land and water management in the Upper Klamath Basin area to improve the quality of water entering the Lower Klamath Basin.

This NPS AMPP covers the portion of the Klamath Basin that is upstream of Iron Gate Dam near Hornbrook, CA, excepting the Lost River and Butte sub-basins. This area was chosen for this assessment because water quality impacts to water quality on the Klamath River primarily occur upstream of this location.

Water Quality, Agriculture, Pollution, Agreements, NPS Management Program Plan
2012ReclamationFinal Biological Assessment and Essential Fish Habitat Determination on the Proposed Removal of Four Dams on the Klamath River, , , , , 180102

This Biological Assessment (BA) and Essential Fish Habitat (EFH) Determination for the Proposed Removal of Four Dams on the Kamath River has been revised from the October 3, 2011 version due to new information being made available, clarification of the proposed federal action, and recommended edits from the United States Fish and Wildlife Service (USFWS) and National Oceanic and Atmospheric Administration’s National Marine Fisheries Service (NMFS). More specifically, the main revisions made to this BA include: 1) clarification that the Klamath Basin Restoration Agreement (KBRA) is not a part of the Proposed Action and therefore, is not analyzed as such in this BA; 2) include section on Standard Operating Procedures (SOPs) and Best Management Practices (BMPs); 3) include information from the May 24, 2012 Technical Memorandum for the Evaluation of Dam Removal and Restoration (EDRRA) model runs on Klamath Chinook abundance forecast and subsequent revisions to Steller sea lion and Southern Resident Distinct Population Segment (DPS) killer whale analysis; 4) revision of determination of effects analysis on marbled murrelet; 5) revisions to Southern DPS eulachon, bull trout, and shortnose and Lost River suckers effects analysis; and 6) add language for proposed revision of northern spotted owl critical habitat.

Biological Assessment, Critical Habitat, Dam Removal, Essential Fish Habitat
2014E. Bayley Toft-DupuyThe Ovidian Water Drop: Negotiations in the Klamath Basin, 180102

The Klamath Basin agreements represent an imperfect, yet workable, framework for water management in the Upper and Lower Klamath Basin. After decades of conflict, the collaborative nature of the agreements provides a vision of stability for stakeholders and a potentially useful model for future water resource conflicts. With dozens of parties involved—including local, state, and federal actors—the agreements represent not only an integrative vision but also a profoundly symbolic redirection for a conflict-ridden basin. Like the water drop hollowing the stone, the ultimate solution in the basin did not spring from force or conflict but emerged, over time, from the perseverance and continual resolve of the parties involved: parties jaded by the status quo and determined to find some version of a sustainable solution.

Negotiations, Land Use, Agreements, Stakeholders
2016PacifiCorpLower Klamath Project – Exhibit M18010209

The Lower Klamath Project area is located on the upper Klamath River in Klamath County (south-central Oregon) and Siskiyou County (north-central California). The nearest principal cities are Klamath Falls, Oregon, located at the northern end of the Project area; Medford, Oregon, 45 miles northwest of the downstream end of the Project; and Yreka, California, 20 miles southwest of the downstream end. Figure M2.1-1 is a map of the Project area. The Lower Klamath Project consists of four developments which are on the Klamath River between river mile (RM) 190 and RM 228. The Lower Klamath Project begins at the J.C. Boyle Development and continues downstream to the Iron Gate Development.

iron gate hatchery, Transmission network, PacifiCorp, Powerhouse, Reservoir
2016Department of the InteriorDepartment Of The Interior letter, 180102

Department of the Interior support of the the application submitted by PacifiCorp and the Klamath River Renewal Corporation and urges the Federal Energy Regulator Commission to approve these applications as a critical step toward resolving the significant water-related issues in the Klamath Basin.

Klamath River Renewal Corporation, PacifiCorp, Dam removal, Secretarial Statement of Support
2003SRFB, Washington Salmon Recovery Funding BoardMonitoring and Evaluation Strategy For Habitat Restoration And Acquisition Projects, ,

The Salmon Recovery Funding Board (SRFB) was established in 1999 to fund salmon habitat restoration and protection projects and related activities. Starting in 2000, the SRFB established policies authorizing the types of projects eligible for funding and an evaluation process for selecting projects. The SRFB, in their Policies and Guidelines, identified implementation, effectiveness, and validation monitoring as key components of their adaptive management model.

This document is intended to address elements of Washington’s Comprehensive Monitoring Strategy (CMS), and it provides:
- Overall SRFB effectiveness and validation monitoring strategy;
- Prioritized monitoring by type and category;
- Estimated costs over the next ten years; and
- SRFB-NOAA Fisheries-OWEB-BPA agreed upon reporting metrics.

Habitat restoration, Monitoring, Evaluation Strategy, Design Criteria
2015IPCCClimate Change 2014 Synthesis Report

The Synthesis Report (SYR) distils and integrates the findings of the three Working Group contributions to the Fifth Assessment Report (AR5) of the Intergovernmental Panel on Climate Change (IPCC), the
most comprehensive assessment of climate change undertaken thus far by the IPCC: Climate Change 2013: The Physical Science Basis; Climate Change 2014: Impacts, Adaptation, and Vulnerability; and Climate
Change 2014: Mitigation of Climate Change. The SYR also incorporates the findings of two Special Reports on Renewable Energy Sources and Climate Change Mitigation (2011) and on Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation (2011).

Climate Change, Risk and Impacts, Adaptation and Mitigation
1999Kier AssociatesMid-term Evaluation Of The Klamath River Basin Fisheries Restoration Program, , , , 180102

This Mid-term Evaluation Of The Klamath River Basin Fisheries Restoration Program is the first in-depth evaluation of the Program since its launch in 1987. It may be the most comprehensive evaluation of any large-scale Pacific salmon restoration program undertaken to date. The two-state Klamath River basin covers ten million acres. Of that area the Klamath Fisheries Restoration Program addresses nearly 3,000,000 watershed
acres.

This evaluation covers not only the biological, but the institutional and political aspects of the Program. The evaluation employs a number of methods, including the use of the Program’s administrative databases, interviews of Program participants, field evaluation of the Program’s restoration projects, and the use of information concerning other, comparable Pacific Coast fisheries restoration programs. The evaluation results are presented in the same order as they appear in the evaluation workplan, with each of the following chapters covering one of the workplan’s nine basic tasks. A tenth chapter, an evaluation of both large and small hatchery operations in the Klamath basin, was developed at the request of the Klamath River Fish and Wildlife Office (KRFWO).

Restoration Program, Fish Management, Upper Basin Amendment, Salmon, Green sturgeon, Habitat Protection,
2009Stillwater SciencesEffects of sediment release following dam removal on the aquatic biota of the Klamath River. Final Technical Report, 180102

Four dams on the Klamath River are under consideration for removal: Iron Gate, Copco 1 and 2, and J.C. Boyle. These dams are located between river miles 196 and 225 in Oregon (J.C. Boyle) and California (Iron Gate, Copco 1 and 2), downstream of the Upper Klamath Lake. Dam removal options currently under consideration would result in 1.3–2.9 million metric tons of fine sediment (sand, silt, and finer) being transported into downstream reaches of the Klamath River (Stillwater Sciences 2008), resulting in high suspended sediment loads, which can result in deleterious effects on aquatic habitats and species. This report first summarizes Stillwater Sciences’s analyses of the physical properties and concentrations of suspended sediment likely to result from sediment releases. It then focuses on the potential biological effects of sediment release on aquatic habitats and species if the dams were to be removed. In addition, opportunities to reduce the impacts of dam removal were explored, and recommendations are presented based on our analysis. The long-term benefits of dam removal (although assumed crucial to recovery of the aquatic biota) were not analyzed as a part of this study.

Dam removal, Aquatic biota, Sediment
2010Stillwater SciencesAnticipated Sediment Release from Klamath River Dam Removal within the Context of Basin Sediment Delivery. Final Report, 180102

Four dams on the Klamath River owned by PacifiCorp (Iron Gate, Copco 1 and 2, and J.C. Boyle) are being considered for removal to improve fish passage and water quality. Numerical modeling under various scenarios predicted that dam removal could release up to 3.2 million tons of reservoir sediment to downstream reaches, the majority of which would be released in the first year following removal (GEC 2006, Stillwater Sciences 2008). Little sedimentation or increase in flood stage heights are expected to occur downstream of Iron Gate Dam (Stillwater Sciences 2008). Additional studies assessed the potential effects of dam removal on fish and water quality in the lower Klamath River (Stillwater Sciences 2009a, Stillwater Sciences 2009b). This study was commissioned by the California State Coastal Conservancy to place them anticipated sediment release from dam removal into the context of background sediment delivery from watershed sources. Specific objectives of the study included (1) summarizing existing information about the quantity and size distribution of background sediment delivery from the watershed to the Klamath River, (2) comparing estimates of the cumulative background sediment delivery with independent estimates of total sediment flux, and (3) comparing modeled estimates of sediment release from dam removal with estimates of background sediment delivery.

The Klamath River traverses 254 mi and drains a 15,722 mi2 area that includes the Modoc Plateau, Cascade Range, Klamath Mountains, and Northern Coast Range. The Klamath River watershed can be divided into upper and lower basins with distinctly different climatic, geologic, geomorphic, and hydrologic characteristics. The geologic boundary between the upper and lower basins occurs a short distance downstream of Iron Gate Dam near Cottonwood Creek.

Sediment Release, Dam Removal, Iron Gate Dam, Geologic and Geomorphic Controls
2011Yantao Cui, Ethan Bell, Maia Singer, Frank LigonQualitative assessment of prolonged facility removal for the Klamath River dams180102

The U.S. Department of the Interior (DOI), as the National Environmental Policy Act (NEPA) lead agency, and the California Department of Fish and Game (DFG), as the California Environmental Quality Act (CEQA) lead agency, are currently developing an Environmental Impact Statement/ Environmental Impact Report (EIS/EIR) for the Klamath Hydroelectric Settlement Agreement (KHSA) and the Klamath Basin Restoration Agreement (KBRA). The EIS/EIR will evaluate the environmental and social effects of a set of alternatives that may include removing all or portions of J.C. Boyle, Copco 1 and 2, and Iron Gate dams on the Klamath River, which would provide volitional fish passage to aid in restoring salmonid fisheries.

The current plan for removing the four dams calls for reservoir drawdown during the winter of 2019 in a controlled manner, releasing the majority of the erodible sediments to the middle and lower Klamath River prior to the summer of 2020. This approach would limit the major fisheries impacts to the winter of 2019 and spring of 2020. Based upon a recent fisheries impacts analysis that considered predicted suspended sediment concentration and duration as well as geographic distribution and life-history traits of focal fish species in the downstream river reaches, suspended sediment impacts would be sub-lethal for most species and life stages, while some species and life stages would experience lethal impacts (Stillwater Sciences 2011).

Some stakeholders involved in the EIS/EIR and Secretarial Determination process have questioned the current dam removal plan and have asked if impacts to aquatic species could be reduced by prolonging the release of erodible sediments over multiple years. A prolonged release period can potentially decrease suspended sediment concentrations at any given point in time but would extend the number of years of relatively high concentrations in the river downstream of the dams.

Qualitative assessment, Staged dam removal, Slow reservoir drawdown, sequenced dam removal, biological considerations
2010Stillwater SciencesPotential Responses of Coho Salmon and Steelhead Downstream of Iron Gate Dam to No-Action and Dam- Removal Alternatives for the Klamath Basin, , , , , , 180102

The intent of this report is to summarize the anticipated effects of fulfilling the terms of both the Klamath Hydropower Settlement Agreement as well as the Klamath Basin Restoration Agreement (i.e., dam removal paired with KBRA actions) on two species of anadromous salmonids: coho salmon (Oncorhynchus kisutch) and steelhead (O. mykiss), as compared with a “no action” alternative. This report will be made available to selected panels of fisheries experts to aid in the Secretarial Determination process. The analysis only addresses potential fish population responses within the Klamath mainstem and tributaries downstream of Iron Gate Dam.

Coho Salmon, Winter Steelhead, Summer Steelhead, Iron Gate Dam, Tributaries, Biological and genetic diversity, Dams-Out Alternative,
2008Stillwater SciencesKlamath River Dam Removal Study: Sediment Transport DREAM-1 Simulation, 180102

Iron Gate, Copco 1, Copco 2, and J.C. Boyle dams, located on the Klamath River in Oregon and California downstream of Upper Klamath Lake, are under consideration for possible removal. Data collected to date indicate that 11.5 to 15.3 million m3 (15 to 20 million cubic yards) of deposits are stored within the four reservoirs (Eilers and Gubala 2003; GEC 2006). Unlike the other mid- to large-sized dam removal projects in the U.S. (e.g., Marmot Dam on the Sandy River, Oregon; dams on the Elwha River, Washington; Matilija Dam on Ventura Creek, California; and San Clemente Dam on Carmel River, California), the deposits in the above four reservoirs on the Klamath River have a high water content (~ 80% by volume), and the majority of the sediment particles are fine-grained (i.e., in the silt and clay range), while the composition of the Klamath River channel bed downstream of these dams are cobble sized (e.g., Stillwater Sciences 2004; Cui et al. 2005; GEC 2006; Shannon and Wilson Inc. 2006). As a result, if the deposits are released downstream, high suspended sediment concentrations and their associated biological impacts due to the quick release of fine sediment will most likely be the major concern (GEC 2006), while concerns for downstream sediment deposition common to other dam removal projects will be minor, as demonstrated by the “worst-case-scenario” assumption analyses conducted in Stillwater Sciences (2004).

Dam removal, Sediment Transport, DREAM-1 Simulation
1997Thomas A. Shaw, Chris Jackson, Dan Nehler, Michael MarshallKlamath River (Iron Gate Dam to Seiad Creek) Life Stage Periodicities for Chinook, Coho and Steelhead, , 180102

This report is a compilation of historic and recent published and unpublished literature, field notes, and personal communications pertaining to life stage periodicities for races of chinook salmon (Onchorhynchus tshawyscha), coho salmon (O. kisutch) and steelhead trout (O. mykiss) in the Klamath River, northern California. Periodicity information is necessary to evaluate the effects of magnitude, duration and timing of discharge from Iron Gate Dam on microhabitat for anadromous salmonids of interest in the Klamath River.

In 1984, periodicities for anadromous salmonids were described for the entire Klamath River Basin based on a round table discussion among personnel of the U.S. Fish and Wildlife Service, U.S. Forest Service, California Department of Fish and Game and several private consulting firms (USFWS 1984a). Since 1984, additional information has been collected by numerous agencies which will aid in refining the periodicities described in that report.

Migration, Spawning, Emergence, Chinook, Coho, Steelhead
2008Dr. Thomas B. HardySupport for the Klamath Settlement Agreement, , , 180102

Support for the Klamath Settlement Agreement, this document in conjunction with several full days of technical discussions by the principal authors in Arcata allowed a detail and comprehensive review prior to the discussions held in Mt. Shasta on April 10th and 11th 2008.

Settlement Agreement
2015Damon H. Goodman, Stewart B. ReidRegional Implementation Plan for Measures to Conserve Pacific Lamprey (Entosphenus tridentatus), California – North Coast Regional Management Unit, , , ,

Pacific Lamprey, Entosphenus tridentatus, were historically widely distributed from Mexico north along the Pacific Rim to Japan. They are culturally important to indigenous people throughout their range, and play a vital role in the ecosystem: cycling marine nutrients, passing primary production up the food chain as filter feeding larvae, promoting bioturbation in sediments, and serving as food for many mammals, fishes and birds. Recent observations of substantial declines in the abundance and range of Pacific Lamprey have spurred conservation interest in the species, with increasing attention from tribes, agencies, and others.

In 2003 the U.S. Fish and Wildlife Service (USFWS) was petitioned by 11 conservation groups to list four species of lamprey in Oregon, Washington, Idaho, and California, including the Pacific Lamprey, under the Endangered Species Act (ESA) (Nawa et al. 2003). The USFWS review of the petition indicated a likely decline in abundance and distribution in some portions of the Pacific Lamprey's range and the existence of both long-term and proximate threats to this species, but the petition did not provide information describing how the portion of the species’ petitioned range (California, Oregon, Idaho, and Washington) or any smaller portion is appropriate for listing under the ESA. The USFWS was therefore unable to define a listable entity based on the petition and determined Pacific Lamprey to be ineligible for listing (USFWS 2004).

Pacific Lamprey (Entosphenus tridentatus), Fish passage, Stream Flow Management,
2017The Nature ConservancyConservation Gateway – Klamath Basin, , , , , , , 180102

The Upper Klamath Basin of southern Oregon contains a vast complex of lakes, rivers and wetlands support tremendous freshwater biodiversity including seventeen native fish species. In addition, the basin is among one of the highest in concentration of groundwater-dependent ecosystems in Oregon. For example, groundwater contributes 86% of the water budget of Klamath Marsh National Wildlife Refuge, and 15% of the inflow to Upper Klamath Lake.

However, flow alteration, habitat loss and water quality degradation have severely impacted aquatic resources. Today, six of the seventeen native fish in the Upper Klamath Basin are extinct, extirpated, or listed as endangered or threatened. A number of plans and agreements have focused attention on restoration of floodplain and wetland habitat, recognizing the importance of the basin.

Habitat Loss, Water Quality, Endangered Suckers, Restoration
2012NewFields River Basin Services, Dr. G. M. KondolfEvaluating Stream Restoration Projects in the Sprague River Basin, , , , , 18010202

Aquatic ecosystems in the Sprague River Basin in southern Oregon have been degraded by historical and current land uses including logging, dam construction, cattle grazing, and agriculture. Since the mid-1990’s, projects have been funded to improve watershed conditions in the Sprague River Basin for affected fish species, including Lost River sucker, shortnose sucker, and redband trout, channel stability, riparian habitat, and water quality. Continuation and potential future expansion of stream restoration projects in the Sprague River Basin warrant a basinwide review of the benefits of previous restoration projects. The purpose of this project was to evaluate the performance of a variety of completed restoration projects in the basin and identify key lessons learned. These lessons will be used to help implement meaningful adaptive management of the basin’s aquatic resources and to guide future project prioritization, planning, and design.

Restoration, Evaluation, Geology, Hydrology, Geomorphology, Organizational Framework, Conceptual Models, Adaptive Management, Guidance for Future Projects
2004Marmorek, David, Ian Parnell, Marc Porter, Christine Pinkham, Clint Alexander, Calvin Peters, Joel Hubble, Charles Paulsen, Timothy FisherA Multiple Watershed Approach to Assessing the Effects of Habitat Restoration Actions on Anadromous and Resident Fish Populations, , ,

Habitat protection and restoration is a cornerstone of current strategies to restore ecosystems, recover endangered fish species, and rebuild fish stocks within the Columbia River Basin. Strategies featuring habitat restoration include the 2000 Biological Opinion on operation of the Federal Columbia River Power System (FCRPS BiOp) developed by the National Marine Fisheries Service (NMFS), the 2000 Biological Opinion on Bull Trout developed by the US Fish and Wildlife Service (USFWS), and Sub- Basin Plans developed under the Fish and Wildlife Program of the Northwest Power and Conservation Council (NWPCC). There is however little quantitative information about the effectiveness of different habitat restoration techniques. Such information is crucial for helping scientists and program managers allocate limited funds towards the greatest benefits for fish populations. Therefore, it is critical to systematically test the hypotheses underlying habitat restoration actions for both anadromous and resident fish populations. This pilot project was developed through a proposal to the Innovative Projects fund of the NWPCC (ESSA 2002). It was funded by the Bonneville Power Administration (BPA) following reviews by the Independent Scientific Review Panel (ISRP 2002), the Columbia Basin Fish and Wildlife Authority (CBFWA 2002), the NWPCC and BPA. The study was designed to respond directly to the above described needs for information on the effectiveness of habitat restoration actions, including legal measures specified in the 2000 FCRPS BiOp (RPA 183, pg. 9-133, NMFS 2000). Due to the urgency of addressing these measures, the timeline of the project was accelerated from a duration of 18 months to 14 months. The purpose of this pilot project was to explore methods for evaluating past habitat restoration actions and their effects on fish populations.

Bull trout, Spring Chinook, Habitat Restoration, alternative multi-watershed designs, Implementation monitoring, Monitoring protocols, Yakima River subbasin, Salmon River, Columbia Basin,
2016Nicolaas Bouwes, Stephen Bennett, Joe WheatonAdapting Adaptive Management for Testing the Effectiveness of Stream Restoration: An Intensively Monitored Watershed Example,

A large effort is underway to test the effectiveness of stream restoration in the Pacific Northwest using intensively monitored watersheds (IMWs) to improve salmonid habitat with the expectation to increase salmonid production (Bennett et al. 2016). How, or whether, stream restoration can improve target salmonid populations and ecosystem functions remains equivocal despite the enormous efforts that have been expended
in implementation of projects throughout North America (Bernhardt et al. 2005; Roni et al. 2008). Restoration efforts applied under adaptive management (AM) frameworks will likely be the most efficient way to better understand the effectiveness of stream restoration, promote accountability within the restoration community and document restoration effectiveness that will guide future restoration strategies (Downs and Kondolf 2002; Rieman et al. 2015). Yet, AM remains underutilized or misapplied in restoration (Allen and Gunderson 2011), and we suspect that this stems from a misunderstanding of what AM is and where it is appropriate to apply and/or a perceived difficulty in developing the framework. Our goal in this essay is to clarify the application of AM and to promote its use in IMWs and restoration projects in general. We briefly review what AM is, the different approaches to implementing AM, and the key elements common to AM. We then provide an example of how we are using AM to test the effectiveness of adding large woody debris (LWD) to increase habitat complexity and increase production of steelhead Oncorhynchus mykiss in the Asotin Creek IMW in Washington.
Oncorhynchus mykiss in the Asotin Creek IMW in Washington.

Adaptive Management, Planning, Evaluation,
2016Stephen Bennett, George Pess, Nicolaas Bouwes, Phil Roni, Robert E. Bilby, Sean Gallagher, Jim Ruzycki, Thomas Buehrens, Kirk Krueger, William Ehinger, Joseph Anderson, Chris Jordan, Brett Bowersox, Correigh GreeneProgress and Challenges of Testing the Effectiveness of Stream Restoration in the Pacific Northwest Using Intensively Monitored Watersheds, ,

Across the Pacific Northwest, at least 17 intensively monitored watershed projects have been implemented to test the effectiveness of a broad range of stream restoration actions for increasing the freshwater production of salmon and steelhead and to better understand fish–habitat relationships. We assess the scope and status of these projects and report on challenges implementing them. We suggest that all intensively monitored watersheds should contain key elements based on sound experimental design concepts and be implemented within an adaptive management framework to maximize learning. The most significant challenges reported by groups were (1) improving coordination between funders, restoration groups, and researchers so that restoration and monitoring actions occur based on the project design and (2) maintaining consistent funding to conduct annual monitoring and evaluation of data. However, we conclude that despite these challenges, the intensively monitored watershed approach is the most reliable means of assessing the efficacy of watershed scale restoration.

restoration, monitoring, intensively monitored watershed (IMW), data management, knowledge transfer, Adaptive management framework
2015Oregon Department of Fish and Wildlife (ODFW)Threatened, Endangered, and Candidate Fish and Wildlife Species

Threatened, Endangered, and Candidate Fish and Wildlife Species published by Oregon Department of Fish and Wildlife, Wildlife division: Regulating harvest, health, and enhancement of wildlife populations.

ODFW, Threatened, Endangered, Candidate Fish, Wildlife Species
2017High Country NewsTribal fishing on the Klamath River, , 180102

The Klamath River flows out of the high deserts of southern Oregon, bending southwest across the state line and then plunging through thickly forested canyons before emptying into the Pacific Ocean on the Northern California coast. Its headwaters are dammed and diverted, mainly for agriculture and electricity generation, but the lower river is home to the third-largest salmon runs in the Continental U.S., as well as populations of steelhead, lamprey, sturgeon and other species. Tribes in the lower basin—the Yurok, Hoopa and Karuk—have long relied upon this fishery and have fought to protect it in the face of habitat loss and ecological degradation. California’s ongoing drought has brought additional stress to an already strained situation, but the river remains an essential source of food and income for many of those who live along it.

Tribal fishing, sturgeon, steelhead, salmon, lamprey, fishing
2016J. Ryan Bellmore, Jeffrey J. Duda, Laura S. Craig, Samantha L. Greene, Christian E. Torgersen, Mathias J. Collins, Katherine VittumStatus and trends of dam removal research in the United States, ,

Aging infrastructure coupled with growing interest in river restoration has driven a dramatic increase in the practice of dam removal. With this increase, there has been a proliferation of studies that assess the physical and ecological responses of rivers to these removals. As more dams are considered for removal, scientific information from these dam-removal studies will increasingly be called upon to inform decisions about whether, and how best, to bring down dams. This raises a critical question: what is the current state of dam-removal science in the United States? To explore the status, trends, and characteristics of dam-removal research in the U.S., we searched the scientific literature and extracted basic information from studies on dam removal. Our literature review illustrates that although over 1200 dams have been removed in the U.S., fewer than 10% have been scientifically evaluated, and most of these studies were short in duration (<4 years) and had limited (1–2 years) or no pre-removal monitoring. The majority of studies focused on hydrologic and geomorphic responses to removal rather than biological and water-quality responses, and few studies were published on linkages between physical and ecological components. Our review illustrates the need for long-term, multidisciplinary case studies, with robust study designs, in order to anticipate the effects of dam removal and inform future decision making.

Dam removal, Biological metrics, Water quality metrics, Physical metrics
2015Jacob W. Malcom, Ya-Wei LiData contradict common perceptions about a controversial provision of the US Endangered Species Act

Separating myth and reality is essential for evaluating the effectiveness of laws. Section 7 of the US Endangered Species Act (Act) directs federal agencies to help conserve threatened and endangered species, including by consulting with the US Fish and Wildlife Service (FWS) or National Marine Fisheries Service on actions the agencies authorize, fund, or carry out. Consultations ensure that actions do not violate the Act’s prohibitions on “jeopardizing” listed species or “destroying or adversely modifying” these species’ critical habitat. Because these prohibitions are broad,many people consider section 7 the primary tool for protecting species under the Act, whereas others believe section 7 severely impedes economic development. This decades-old controversy is driven primarily by the lack of data on implementation: past analyses are either over 25 y old or taxonomically restricted. We analyze data on all 88,290 consultations recorded by FWS from January 2008 through April 2015. In contrast to conventional wisdom about section 7 implementation, no project was stopped or extensively altered as a result of FWS finding jeopardy or adverse modification during this period. We also show that median consultation duration is far lower than the maximum allowed by the Act, and several factors drive variation in consultation duration. The results discredit many of the claims about the onerous nature of section 7 but also raise questions as to how federal agencies could apply this tool more effectively to conserve species. We build on the results to identify ways to improve the effectiveness of consultations for imperiled species conservation and increase the efficiency of consultations.

US Endangered Species Act
2016National Marine Fisheries ServiceDraft Eulachon Recovery Plan October 2016. Endangered Species Act Recovery Plan for the Southern Distinct Population Segment of Eulachon (Thaleichthys pacificus), , , , ,

This Recovery Plan serves as a blueprint for the protection and recovery of the southern Distinct Population Segment (DPS) of eulachon (Thaleichthys pacificus) using the best available science per the requirements of the Endangered Species Act (ESA). The Recovery Plan links management actions to an active research program to fill data gaps and a monitoring program to assess these actions’ effectiveness. Research and monitoring results will provide information to refine ongoing actions and prioritize new actions to achieve the Plan’s goal: to restore the listed species to the point where it no longer requires the protections of the ESA.

The goal of this Recovery Plan is to increase the abundance and productivity of eulachon, and to protect and enhance the genetic, life history, and spatial diversity of eulachon throughout its geographical range while sufficiently abating threats to warrant delisting of the species. The objectives are:
1. Ensure subpopulation viability.
2. Conserve spatial structure and temporal distribution patterns.
3. Conserve existing genetic and life history diversity and provide opportunities for interchange of genetic material between and within subpopulations.
4. Eliminate or sufficiently reduce the severity of threats.

Endangered Species Act (ESA), eulachon, Thaleichthys pacificus, adaptive management
2017Conservation Biology InstituteData Basin

Data Basin is a science-based mapping and analysis platform that supports learning, research, and sustainable environmental stewardship. As environmental conservation problems become more serious and the demand to solve them grows more urgent, it is critical that science, practice, policy, and people are integrated in stronger ways. A team of scientists, software engineers, and educators at the Conservation Biology Institute (CBI) built Data Basin with the strong conviction that we can expand our individual and collective ability to develop sustainable solutions by empowering more people through access to spatial data, non-technical tools, and collaborative networks.

- Explore and organize data & information
- Create custom visualizations, drawings, & analyses
- Use collaborative tools in groups
- Publish datasets, maps, & galleries
- Develop decision-support and custom tools

Data Basin is used by over 17000 scientists, natural resource practitioners, students & educators, and interested citizens from diverse sectors and geographies.

research, sustainable environmental stewardship, spatial data, collaborative networks
2003Oregon Historical SocietyThe Oregon History Project – Sucker Harvest

For thousands of years, the Lost River suckers and shortnose suckers have been important to the Klamath Indian culture and essential to their subsistence. In 1983, the Klamath Indian Tribes, Oregon Department of Fish and Wildlife, and U.S. Fish and Wildlife Service jointly initiated a biological study of Klamath Basin suckers. The data concluded that the sucker population was decreasing due to poor water quality and levels in Upper Klamath Lake. This prompted the Klamath Tribes to restrict their sucker fishing in 1985, and by the next year, tribal leaders agreed to terminate all sucker fishing. Rather than hold their traditional sucker harvest celebrations, as pictured here in 1905, the Klamath Tribes today hold “Return of the C’wam” (Klamath language for the Lost River sucker, pronounced “cha-wam”) ceremonies.

The decision to curtail irrigation water to Klamath Reclamation Project users in 2001 was based on a federally mandated Biological Opinion that determined that Project water was needed to protect endangered coho salmon and Lost River and shortnose suckers. The events of 2001, however, polarized Klamath Basin communities and created conflicts between farmers and conservationists, farmers and government agencies, and farmers and tribal members. During the spring and summer of 2001, faculty from Oregon State University and the University of California Cooperative Extension studied the economic, social, institutional, and natural consequences of the Klamath Basin crisis. They interviewed, among other groups, Klamath Basin Native Americans, all of whom recounted recent incidents where tribal members were shunned or treated badly by non-Natives. Some were threatened with guns and run off the road in retaliation for the water restrictions. In one case, a tribesman was beaten by non-Natives. Tribal officials advised members to walk away from arguments or other tense situations.

Suckers
2015J.E. O’Connor, J. J. Duda , G. E. Grant1000 dams down and counting

Forty years ago, the demolition of large dams was mostly fiction, notably plotted in Edward Abbey’s novel The Monkey Wrench Gang. Its 1975 publication roughly coincided with the end of large-dam construction in the United States. Since then, dams have been taken down in increasing numbers as they have filled with sediment, become unsafe or inefficient, or otherwise outlived their usefulness. Last year’s removals of the 64-m-high Glines Canyon Dam and the 32-m-high Elwha Dam in northwestern Washington State were among the largest yet, releasing over 10 million cubic meters of stored sediment. Published studies conducted in conjunction with about 100 U.S. dam removals and at least 26 removals outside the United States are now providing detailed insights into how rivers respond). A major finding is that rivers are resilient, with many responding quickly to dam removal. Most river channels stabilize within months or years, not decades (4), particularly when dams are removed rapidly; phased or incremental removals typically have longer response times. The rapid physical response is driven by the strong upstream/downstream coupling intrinsic to river systems. Reservoir erosion commonly begins at knickpoints, or short steep reaches of channel, that migrate upstream while cutting through reservoir sediment. Substantial fractions of stored reservoir sediment—50% or more—can be eroded within weeks or months of breaching. Sediment eroded from reservoirs rapidly moves downstream. Some sediment is deposited downstream, but is often redistributed within months. Many rivers soon trend toward their pre-dam states.

Dam removal
2013United States Fish and Wildlife Service (USFWS) - Yreka Fish and Wildlife OfficeStatus of Native Anadromous Fish Species of the Klamath River Basin180102

Chinook salmon are currently the most economically important commercial fishery resource in the Klamath River, and are caught in ocean fisheries from Monterey Bay to the Columbia River. In the Klamath Basin, Chinook currently follow two life history patterns. “Spring Chinook” return from the ocean in the spring, and spend the summer making their way to higher portions of the watershed, where they spawn in August-September. Before the construction of dams on the Klamath River, spring Chinook were the dominant salmon race in the Upper Klamath Basin, but they have been reduced to one dwindling wild run in the Salmon River subbasin and a hatchery run in the Trinity River.

“Fall Chinook” return from the ocean in September and spawn October-November in the main stem rivers and large tributaries. Most Chinook juveniles migrate to the ocean in the late spring of their first year, avoiding the hazards of summer rearing.

Chinook Salmon, fall chinook run, spawning success, spring chinook run
2017Oregon Institute of TechnologyKlamath Waters Digital Library, , 180102

Welcome to the Klamath Waters Digital Library, an online repository of information resources related to water issues in the Klamath Watershed. The digital library encompasses a collection of full-text documents, reports, articles, photographs and maps from the 1800s to the present as well as many special collections. Topics covered include water allocation, land and endangered species management, and the history and development of Klamath Reclamation Project.

Digital Library, Water Allocation, Endangered species management
2017NOAAPacific Northwest Salmon Habitat Project Database, ,

Pacific Northwest Salmon Habitat Project Database. This is a public site for exploring, querying, and downloading fiscal, location, work type, and metric information for salmon habitat restoration projects in the Pacific Northwest is currently in development. The database currently contains spatially referenced, project-level data on over 26,000 restoration actions initiated at over 42,000 locations in the last 15 years (98% of projects report start or end dates in the last 15 years) in the states of Washington, Oregon, Idaho and Montana, USA.

Across the Pacific Northwest, both public and private agents are working to improve riverine habitat for a variety of reasons, including improving conditions for threatened and endangered salmon. These projects are moving forward with little or no knowledge of specific linkages between restoration actions and the responses of target species. Targeted effectiveness monitoring of these actions is required to redress this lack of mechanistic understanding, but such monitoring is in turn dependent on detailed restoration information such as implementation monitoring. We created a standardized data dictionary of project types now being applied throughout the region (now RPA 73 in the FCRPS Biop) to assemble a standardized database of restoration projects. The database was designed specifically to address the needs of regional monitoring programs that evaluate the effectiveness of restoration actions.

This database is maintained by the Northwest Fisheries Science Center's Mathematical Biology and Systems Monitoring Program within the Conservation Biology Division.

Salmon, Restoration, Database, Habitat Restoration
2017CalFishCalFish Data Portal,

The CalFish Mission is to create, maintain, and enhance high quality, consistent data that are directly applicable to policy, planning, management, research, and recovery of anadromous fish and related aquatic resources in California; and to provide data and information services in a timely manner in formats that meet the needs of users. CalFish is a cooperative program involving a growing number of agency and organization partners. Such cooperative support has and will continue to guide the future development of CalFish and ensure the longevity and continued usefulness of the CalFish site.

There are many programs in California that are actively gathering, compiling and analyzing fish and aquatic habitat data. Bringing all of this information together and making it available to a variety of users is crucial to the success of fisheries and habitat monitoring, evaluation, and management within the state. Centralizing access to California fisheries data makes it much easier to develop and maintain state-wide data standards and promote further development of related data programs in California. CalFish addresses the needs of a variety of natural resource management agencies by serving as both data publisher and data clearinghouse, providing access to original data and links to sites with related fish and aquatic habitat information.

CalFish provides direct access to many different types of data relating to fish and aquatic habitat data. These data include categories such as: Population monitoring, Distributions, Migration barriers, Hatcheries, Species recovery, Habitat monitoring, Habitat restoration, Genetics. Users are able to view these data via two basic methods: querying the database tables directly or querying the data geographically.

policy, planning, management, research, recovery, anadromous fish
2017Five Counties Salmonid Conservation ProgramFive Counties Salmonid Conservation Program, 180102

The goal of the Five Counties Salmonid Conservation Program (5C) is to seek opportunities to contribute to the long-term recovery of salmon and steelhead in Northern California. 5C is a project of the Northwest California Resource Conservation & Development Council.

5C and/or member counties coordinate numerous fish passage improvement, sediment reduction, habitat enhancement, and water quality improvement projects in the Program's area in collaboration with 5C partners. Listed below are projects (completed, in progress, and future). They are labeled Fish Passage Improvement Projects (FPIP) and/or Sediment Reduction (SedRed). Listings with no comments are in development and pending. Click on links in projects lists for more details in the 5 areas.

Conservation, Salmon, Steelhead
2004United States Department of Agriculture - Natural Resources Conservation ServiceWork Plan for Adaptive Management Klamath River Basin Oregon & California, , 180102

In the spring of 2001 drought and impacts of the Endangered Species Act prompted the U.S. Bureau of Reclamation to discontinue supplying project irrigation water to over 1,300 farms and ranches in the Klamath Basin. The Natural Resources Conservation Service (NRCS) immediately provided technical and financial assistance to these producers to minimize drought impacts. In cooperation with the Conservation Districts and landowners, NRCS was able to establish 41,000 acres of cover crops on highly erodible lands using Emergency Watershed Protection Program funds. The Klamath Basin conservation districts in Oregon and California then requested NRCS assistance in developing a strategy to mitigate the impacts of drought on agriculture in the Klamath Basin. Later that year, the first of a series of strategic planning sessions was held. From these meetings, the local conservation districts developed a list of mutual resource goals and objectives for the Klamath. To mitigate the effects of the drought on agriculture, conservation districts throughout the 10-million acre Klamath Basin have focused on four resource concerns: (1) decreasing the amount of water needed for agriculture, (2) increasing water storage, (3) improving water quality, and (4) developing fish and wildlife habitat. To achieve these objectives, the conservation districts need timely, quality resource information with which to make decisions, set priorities, and determine the best conservation activities. The future conservation activities and accomplishments, however, will be subject to the availability of funding.

Adaptive Management, conservation, long-term demand, basin wide planning
2016Pacific Fishery Management CouncilPacific Coast Salmon Fishery Management Plan,

This document is the Pacific Coast Salmon Fishery Management Plan, a fishery management plan (FMP) of the Pacific Fishery Management Council (Council or PFMC) as revised and updated for implementation in 2013 and beyond. It guides management of commercial and recreational salmon fisheries off the coasts of Washington, Oregon, and California. Since 1977, salmon fisheries in the exclusive economic zone (EEZ) (three to 200 miles offshore) off Washington, Oregon, and California have been managed under salmon FMPs of the Council. Creation of the Council and the subsequent development and implementation of these plans were initially authorized under the Fishery Conservation and Management Act of 1976. This act, now known as the Magnuson- Stevens Fishery Conservation and Management Act (Magnuson-Stevens Act; MSA), was amended by the Sustainable Fisheries Act (SFA) in 1996, and most recently amended by the Magnuson-Stevens Fishery Conservation and Management Reauthorization Act (MSRA) in 2007. The plan presented in this document contains or references all the elements required for an FMP under the MSA. It completely replaces the 1999 version of the Pacific Coast Salmon Plan.

FMP, PFMC, NOAA, Conservation, Fish Habitat, Bycatch,
2007National Marine Fisheries Service, NOAA, ConservationMagnuson-Stevens Reauthorization Act Klamath River Coho Salmon Recovery Plan, 180102

Built on the foundation of the extensive work already accomplished, NMFS has relied heavily on the existing recovery strategies developed by CDFG (2004) for coho salmon using substantial local stakeholder participation to develop this MSRA Recovery Plan. Our overview of coho salmon life history information available for the Klamath River Basin in Section III found that typical of large river systems, adult coho salmon have a broad period of freshwater entry in the Klamath River and juvenile coho salmon have a strong tendency to redistribute within the Klamath River Basin due to seasonal changes in conditions. Although information on coho salmon population trends in the Klamath River Basin remains incomplete, the available data suggest that coho salmon stock abundance remains at low levels and depressed, with one coho salmon brood year class considerably stronger than the other two brood year classes. This MSRA Recovery Plan should serve as a valuable tool for NMFS development of its SONCC coho salmon recovery plan under the ESA. For instance, the MSRA Recovery Plan summarizes ongoing threats affecting Klamath River coho salmon and current conservation efforts throughout the Klamath River Basin, as well as provides up-to-date scientific information on coho salmon status and trends.

Coho Salmon, Conservation, NMFS, Restoration activities
2014NOAAKlamath River Basin 2014 Report to Congress, , , 180102

The Magnuson-Stevens Fishery Conservation and Management Reauthorization Act of 2006 required NOAA’s National Marine Fisheries Service (NMFS) to develop a recovery plan for Klamath River coho salmon in 2007 and submit annual reports to Congress beginning in 2009. This document is the fifth annual Klamath River Basin Report to Congress. The report updates information presented in the 2012 annual report with information for the calendar years 2012 and 2013 and includes: (1) the actions taken under the recovery plan and other laws relating to recovery of Klamath River coho salmon (Oncorhynchus kisutch), and how those actions are specifically contributing to its recovery; (2) the progress made on the restoration of salmon spawning habitat, including water conditions as they relate to salmon health and recovery, with emphasis on the Klamath River and its tributaries below Iron Gate Dam; (3) the status of other Klamath River anadromous fish populations, particularly Chinook salmon; and (4) the actions taken by the Secretary of Commerce (Secretary) to address the calendar year 2003 National Research Council (NRC) recommendations regarding monitoring and research on Klamath River Basin salmon stocks.
The Klamath River Basin supports Chinook salmon, coho salmon, and steelhead populations, among other anadromous species (e.g., North American green sturgeon (Acipenser medirostris), and eulachon (Thaleichthys pacificus)). Historically, anadromous fish populations supported important commercial, recreational, and tribal fisheries. However, many anadromous fish populations have declined substantially in abundance, and the restoration of these populations will require strong partnerships and collaboration between agencies and stakeholders throughout the basin. One of the target stocks of the ocean mixed-stock recreational and commercial salmon fisheries is the Klamath River fall Chinook salmon.

Coho Salmon, Steelhead, Chinook Salmon, NMFS, SONCC, USFWS
2017Official U.S. Department of the InteriorSecretarial Determination Studies, , , , , , , , , , , , , , , , , , , , , , , , , , 180102

This is the official website of the Department of the Interior, and other federal and state agencies that are involved in carrying out obligations set forth in the Klamath Hydroelectric Settlement Agreement (KHSA), including the Secretarial Determination on Klamath River dams.

Technical Studies and Data for Secretarial Determination Process provides the following reports:

- Secretarial Determination Studies - Final Secretarial Determination Overview Report (October 2012) - Final Klamath Dam Removal Overview Report for the Secretary of the Interior: an Assessment of Science and Technical Information.

The following studies/reports have been conducted as part of the Secretarial Determination Process:

- Engineering, Geomorphology/Construction Studies & Information
- Water Quality Studies & Information
- Background Information on Sediments
- Biological (Fish and Wildlife) Studies & Information
- Economic Studies & Information
- Cultural/Tribal Reports (Associated with Federally Recognized Tribes)
- Real Estate Studies & Information
- Additional Background Documents

KHSA, KBRA, NEPA, CEQA, Restoration, Agreements, Secretarial Determination Studies, Tribal Reports, Water Quality, Economic Studies, Sediments, Geomorphology, Real Estate, Cultural Values, Greenhouse Gas Emissions, Myxozoan Disease, FEMA
2003OWEBOWEB Prioritization Framework Improvement Priorities at Basin and Watershed Scales: Draft OWEB Prioritization Process V 4.2, ,

OWEB contracted to develop a framework that establishes improvement priorities at regional geographic scales and evaluates the relative merits of proposed improvement projects at local watershed scales. OWEB is required by statute to establish regional priorities that will guide funding decisions by the Board (ORS 5431.371 (1) (c)). In addition, OWEB’s Board clarified its funding goal in a “grant funding preference criterion” in September 2001. The Board agreed that, “Capital expenditure project funding priorities will primarily focus on addressing those factors in the watershed that directly limit the improvement of water quantity and water quality and the recovery of fish species listed under the state or federal Endangered Species Act.” The contracted work developed a Prioritization Framework that reflects this preference. The framework is founded on principles of conservation biology and applicable to all basins. It has been tested in two pilot basins. The protection of functioning habitats is an important goal, and should work in concert with improvement actions; however, this project concentrates on identifying watershed improvement project priorities and not habitat protection actions. A separate and concurrent OWEB project designed to identify habitat protection priorities has been initiated. This prioritization project complements the identification of habitat protection actions developed through the Land Acquisition Pilot by providing a framework for identifying regional watershed improvement priorities. This project was designed to create the following two products: Part I. Project Prioritization Framework and Part II. Basin and Watershed Scale Improvement Priorities

Project Prioritization Framework, Basin and Watershed Scale Improvement Priorities, restoration, Watershed Enhancement, Rehabilitation, Winter Steelhead, Summer Steelhead, Spring Chinook, Fall Chinook, Chum
2008D. H. Goodman, S. B. Reid, M. F. Dockers, G. R. Haas, A. P. KinzigerMitochondrial DNA evidence for high levels of gene flow among populations of a widely distributed anadromous lamprey Entosphenus tridentatus (Petromyzontidae)

Mitochondrial DNA variation among 1246 individuals of Pacific lamprey (Entosphenus tridentatus) from 81 populations spanning 2600 km from the Skeena River, British Columbia, to the Ventura River, California, was surveyed using five restriction enzymes. A total of 29 composite haplotypes was detected in two gene fragments (ND2 and ND5). The three most common haplotypes, occurring in 91% of all samples, were present at similar frequencies in all regions. Samples were divided into six biogeographic regions based on sample distribution and geographical landmarks to assess geographic genetic structure. Analysis of molecular variance indicated that 99% of the genetic variation was explained by variability within drainages. The lack of geographical population structure is likely related to a life-history pattern that includes a prolonged larval freshwater stage, migration to oceanic feeding and return to fresh water to spawn. The lack of strong natal homing apparently promotes gene flow among drainages and regions.

Entosphenus tridentatus, genetic variation, Lampetra tridentata, mitochondrial DNA, Pacific lamprey, phylogeography
2016Nicholas A. Som, Nicholas J. Hetrick, J. Scott Foott, Kimberly TrueResponse to Request for Technical Assistance – Prevalence of C. shasta Infections in Juvenile and Adult Salmonids18010209

The Arcata Fish and Wildlife Office (AFWO) Fisheries Program is working with its scientific co-investigators to develop a series of four technical memorandums that summarize recent findings of studies that contribute to our current understanding of Ceratanova shasta (syn Ceratomyxa shasta) infections in the Klamath River, in response to requests for technical assistance from the Yurok and Karuk tribes. Each of the topics addressed in the four technical memorandums: 1) geomorphic channel conditions and flow, 2) polychaete distribution and infections, 3) actinospore and myxospore concentrations, and 4) prevalence of C. shasta
infections in juvenile and adult salmonids, were identified in a conceptual model diagram (Figure 1) taken from Foott et al. (2011), and as discussed with the requesting tribes. The intent of the technical memorandums is to provide managers with a contemporary understanding of the state of the science with regard to the C. shasta in the Klamath River, and to provide a scientific basis to inform and support resource management decisions. In this technical memorandum, we summarize the state of the science regarding the infection and mortality experience of salmonids exposed to C. shasta in the Klamath River.

Parvicapsula minibicornis, Ceratanova shasta
2016Aaron T. David, Stephen A. Gough, William D. PinnixSummary of Abundance and Biological Data Collected During Juvenile Salmonid Monitoring on the Mainstem Klamath River Below Iron Gate Dam, California, 2014, , 18010209

This report summarizes results from the 2014 season of juvenile salmonid outmigrant monitoring on the mainstem Klamath River below Iron Gate Dam. Trapping occurred at three locations: below the confluence with Bogus Creek (river km 308), where Interstate 5 crosses the Klamath River (river km 294), and near the Kinsmen Creek confluence upstream of the confluence with the Scott River (river km 238). Both frame nets and rotary screw traps were used to sample juvenile salmonids and other fishes. Traps were operated beginning in mid- to late February and continued through mid-May or early June. Juvenile salmonids were enumerated daily when traps were operating and subsamples of salmonids were measured for length and weight. Non-salmonid fishes were also enumerated. Mark-recapture studies were conducted periodically at each trap site throughout the season to estimate trap efficiency. The efficiency estimates were combined with the catch data to estimate weekly and seasonal outmigration abundance of natural-origin age-0 juvenile Chinook Salmon at each trap site using a Bayesian time-stratified spline population estimation method. For the periods that traps were operated, abundance estimates of natural-origin age-0 Chinook Salmon were approximately 2.5 million at the Bogus trap site, 2.9 million at the I-5 trap site, and 5.3 million at the Kinsman trap site.

Klamath River, Salmon, Chinook, Coho, Steelhead, Frame Net, Rotary Screw Trap, Juvenile, Outmigrant, Mark-Recapture, Trap Efficiency, Stream Salmonid Simulator
2015Mark D. MagnesonKlamath and Trinity River Intra-Gravel Water Temperatures, 2014 and 2015, , , 180102

Temperature recorders were used to monitor water temperatures in spawning gravels (intra-gravel) and in the water column above spawning gravels (surface) in the Klamath and Trinity Rivers from September 2014 to late June 2015. Water temperature recorders were installed in areas having high densities of Chinook Salmon redds to assess potential differences in predicted embryo incubation and subsequent emergence timing calculated using intra-gravel versus surface water temperatures. In general, intra-gravel water temperatures were warmer in the fall and early winter and cooler in the spring than surface water temperatures. Findings of this study are important given the influence of intra-gravel water temperatures within redds on the development of salmonid embryos and the resulting influence on timing of emergence.

Intra-Gravel, Klamath River, Trinity River, Chinook Salmon, Water Temperature
2016Julie D. Alexander, Jerri L. Bartholomew, Katrina A. Wright, Nicholas A. Som, and Nicholas J. HetrickIntegrating models to predict distribution of the invertebrate host of myxosporean parasites

Manayunkia speciosa, a freshwater polychaete, is the invertebrate host of myxosporean parasites that negatively affect salmonid populations in the Pacific Northwest of the USA. Factors that drive the distribution of M. speciosa are not well understood, which constrains our understanding of disease dynamics and the development of management solutions. We described the distribution of M. speciosa at 3 sites on the Klamath River, California, based on 2-dimensional hydraulic models (2DHMs) and a generalized linear mixed model (GLMM). 2DHMs were built to explain hydraulic variation at each site and used to stratify biological sampling effort along depth–velocity gradients and by substrate class. We assessed the presence/absence of M. speciosa at 362 georeferenced locations in July 2012 and built GLMMs to describe relationships between hydraulic and substrate variables and the distribution of M. speciosa. The best-fitting GLMMs demonstrated that M. speciosa distributions were associated with depth–velocity conditions and substrate size during base discharge (area under the receiver operating characteristic curve [AUC] = 0.88) and at peak discharge (AUC = 0.86). We evaluated the GLMMs with an independent data set collected in July 2013 (n = 280) and found that the top models predicted the distribution of M. speciosa with a high degree of accuracy (AUC = 0.90). These results support the conclusion that the summer distribution of M. speciosa is related to observed hydraulic and substrate conditions during base discharge (summer) and modeled hydraulic and substrate conditions during peak discharge (late winter to early spring). These results may have implications for the use of flow manipulation as a disease management tool. These results also illustrate the importance of examining species distribution data in the context of temporally disconnected environmental factors and demonstrate how models can fulfill this need.

parasites, Manayunkia speciosa, salmonid disease, enteronecrosis, Ceratonova shasta, Parvicapsula minibicornis, two-dimensional hydraulic model,
2015Mark D. MagnesonKlamath River Flow and Water Temperature, Water Year 2012, , , 180102

Water temperature was monitored at several locations in the Klamath Basin from April to October 2012. The uppermost Klamath River site was located upstream of Copco 1 Reservoir on the mainstem Klamath River, and the lowermost site was established just upstream of the Klamath Estuary near Klamath, CA. The highest daily mean water temperature recorded on the mainstem Klamath during the period of study was 24.6°C at Happy Camp, CA on August 5 and 17. Of three tributaries sampled, the Shasta River recorded the highest daily mean water temperature at 26.0°C, but only had a slight influence on mainstem water temperatures due to its low relative volume. Mainstem water temperatures peaked about two weeks later than the past 10-yr mean (2002-2011). Augmented flow releases from Lewiston Dam on the Trinity River were used to reduce risk of a potential fish kill in the lower Klamath River and significantly reduced Klamath River water temperatures during implementation.

water temperature, river flow
2014R. Adam Ray, RussellW. Perry, Nicholas A. Som, Jerri L. BartholomewUsing Cure Models for Analyzing the Influence of Pathogens on Salmon Survival

Parasites and pathogens influence the size and stability of wildlife populations, yet many population models ignore the population-level effects of pathogens. Standard survival analysis methods (e.g., accelerated failure time models) are used to assess how survival rates are influenced by disease. However, they assume that each individual is equally susceptible and will eventually experience the event of interest; this assumption is not typically satisfied with regard to pathogens of wildlife populations. In contrast, mixture cure models, which comprise logistic regression and survival analysis components, allow for different covariates to be entered into each part of the model and provide better predictions of survival when a fraction of the population is expected to survive a disease outbreak.We fitted mixture cure models to the host–pathogen dynamics of Chinook Salmon Oncorhynchus tshawytscha and Coho Salmon O. kisutch and the myxozoan parasite Ceratomyxa shasta. Total parasite concentration, water temperature, and discharge were used as covariates to predict the observed parasite-induced mortality in juvenile salmonids collected as part of a long-term monitoring program in the Klamath River, California. The mixture cure models predicted the observed total mortality well, but some of the variability in observed mortality rates was not captured by the models. Parasite concentration and water temperature were positively associated with total mortality and the mortality rate of both Chinook Salmon and Coho Salmon. Discharge was positively associated with total mortality for both species but only affected the mortality rate for Coho Salmon. The mixture cure models provide insights into how daily survival rates change over time in Chinook Salmon and Coho Salmon after they become infected with C. shasta.

Coho Salmon, Chinook Salmon, parasites, pathogens, mortality
2014Nicholas A. Soma, Pascal Monestiez, Jay M. Ver Hoef, Dale L. Zimmerman, Erin E. PetersonSpatial sampling on streams: principles for inference on aquatic networks, ,

For ecological and environmental data, prior inquiries into spatial sampling designs have considered two-dimensional domains and have shown that design optimality depends on the characteristics of the target spatial domain and intended inference. The structure and water-driven continuity of streams prompted the development of spatial autocovariance models for stream networks. The unique properties of stream networks, and their spatial processes, warrant evaluation of sampling design characteristics in comparison with their two-dimensional counterparts. Common inference scenarios in stream networks include spatial prediction, estimation of fixed effects parameters, and estimation of autocovariance parameters, with prediction and fixed effects estimation most commonly coupled with autocovariance parameter estimation. We consider these inference scenarios under a suite of network characteristics and stream-network spatial processes. Our results demonstrate, for parameter estimation and prediction, the importance of collecting samples from specific network locations. Additionally, our results mirror aspects from the prior two-dimensional sampling design inquiries, namely, the importance of collecting some samples within clusters when autocovariance parameter estimation is required. These results can be applied to help refine sample site selection for future studies and further showcase that understanding the characteristics of the targeted spatial domain is essential for sampling design planning.
been contributed to by US Government employees and their work is in the public domain in the USA.

sampling design, spatial statistics, stream networks
2012John Beeman, Steven Juhnke, Greg Stutzer, Katrina WrightEffects of Iron Gate Dam Discharge and Other Factors on the Survival and Migration of Juvenile Coho Salmon in the Lower Klamath River, Northern California, 2006–09, , , 18010209

Current management of the Klamath River includes prescribed minimum discharges intended partly to increase survival of juvenile coho salmon during their seaward migration in the spring. To determine if fish survival was related to river discharge, we estimated apparent survival and migration rates of yearling coho salmon in the Klamath River downstream of Iron Gate Dam. The primary goals were to determine if discharge at Iron Gate Dam affected coho salmon survival and if results from hatchery fish could be used as a surrogate for the limited supply of wild fish. Fish from hatchery and wild origins that had been surgically implanted with radio transmitters were released into the Klamath River at river kilometer 309 slightly downstream of Iron Gate Dam. Tagged fish were used to estimate apparent survival between, and passage rates at, a series of detection sites as far downstream as river kilometer 33. Conclusions were based primarily on data from hatchery fish, because wild fish were only available in 2 of the 4 years of study. Based on an information-theoretic approach, apparent survival of hatchery and wild fish was similar, despite differences in passage rates and timing, and was lowest in the 54 kilometer (km) reach between release and the Scott River. Models representing the hypothesis that a short-term tagging- or handling-related mortality occurred following release were moderately supported by data from wild fish and weakly supported by data from hatchery fish. Estimates of apparent survival of hatchery fish through the 276 km study area ranged from 0.412 (standard error [SE] 0.048) to 0.648 (SE 0.070), depending on the year, and represented an average of 0.790 per 100 km traveled. Estimates of apparent survival of wild fish through the study area were 0.645 (SE 0.058) in 2006 and 0.630 (SE 0.059) in 2009 and were nearly identical to the results from hatchery fish released on the same dates.

Coho Salmon, survival rates
2012John W. Beeman, Brian Hayes, Katrina WrightDetection Probability of an In-Stream Passive Integrated Transponder (PIT) Tag Detection System for Juvenile Salmonids in the Klamath River, Northern California, 2011180102

A series of in-stream passive integrated transponder (PIT) detection antennas installed across the Klamath River in August 2010 were tested using tagged fish in the summer of 2011. Six pass-by antennas were constructed and anchored to the bottom of the Klamath River at a site between the Shasta and Scott Rivers. Two of the six antennas malfunctioned during the spring of 2011 and two pass-through antennas were installed near the opposite shoreline prior to system testing. The detection probability of the PIT tag detection system was evaluated using yearling coho salmon implanted with a PIT tag and a radio transmitter and then released into the Klamath River slightly downstream of Iron Gate Dam. Cormack-Jolly-Seber capture-recapture methods were used to estimate the detection probability of the PIT tag detection system based on detections of PIT tags there and detections of radio transmitters at radio-telemetry detection systems downstream. One of the 43 PIT- and radio-tagged fish released was detected by the PIT tag detection system and 23 were detected by the radio-telemetry detection systems. The estimated detection probability of the PIT tag detection system was 0.043 (standard error 0.042). Eight PIT-tagged fish from other studies also were detected. Detections at the PIT tag detection system were at the two pass-through antennas and the pass-by antenna adjacent to them. Above average river discharge likely was a factor in the low detection probability of the PIT tag detection system. High discharges dislodged two power cables leaving 12 meters of the river width unsampled for PIT detections and resulted in water depths greater than the read distance of the antennas, which allowed fish to pass over much of the system with little chance of being detected. Improvements in detection probability may be expected under river discharge conditions where water depth over the antennas is within maximum read distance of the antennas.

PIT tagging, Radio-Telemetry
2012Charles D. Chamberlain, Shane Quinn, Billy MatiltonDistribution and Abundance of Chinook Salmon Redds in the Mainstem Trinity River 2002 to 2011, , 18010209

Salmon redds were mapped and carcasses collected in the mainstem Trinity River each fall 2002 through 2011 to quantify and spatially characterize Chinook salmon spawning in the mainstem Trinity River. We applied generalized additive models to the spatiotemporal distribution of hatchery marked or unmarked spawned female salmon carcasses to apportion redd numbers for natural origin and hatchery origin Chinook salmon. These data serve as baseline for the Trinity River Restoration Program to evaluate response of spawning distributions to river rehabilitation and other management actions. Eighteen river rehabilitation sites between Lewiston Dam and the North Fork Trinity River have been implemented over the course of this study. Though spawning distribution responded to physical alterations on a local feature scale (salmon constructed redds in newly created side channels for example), the proportion of redds constructed within the up and downstream boundaries of these rehabilitation sites had not yet significantly changed at broader reach scales. High density spawning area locations remained consistent year to year with little exception. We observed an increase in the mean distance from Lewiston Dam for construction of natural origin Chinook salmon redds over the course of this study. The distribution of hatchery origin Chinook salmon redds remained highly skewed toward Lewiston Dam and Trinity River Hatchery. The number of redds estimated to be constructed by natural origin Chinook salmon females ranged from as low as 2,249 in 2005 to as high as 5,312 in 2011. Estimates of those constructed by hatchery origin Chinook salmon females ranged from as low as 350 in 2009 to as high as 2,269 in 2003. There was no relationship observed in distance downstream of Lewiston Dam that Chinook salmon constructed redds and the yearly total number of Chinook salmon redds.

Salmon redds, Chinook salmon, Trinity River Restoration Program
2013Stephen A. Gough, Samuel C. WilliamsonFall Chinook Salmon Run Characteristics and Escapement for the Main-Stem Klamath River, 2001-2010, 180102

Adult fall-run Chinook salmon (Oncorhynchus tshawytscha) carcasses were surveyed on the mid-Klamath River during spawning seasons 2001 through 2010 to estimate annual escapement using postmortem tag-recovery statistical methods and to characterize the age and sex compositions and spawning success of the runs. The study area consisted of eight consecutive reaches extending 21.2 river km from Iron Gate Dam downriver to the Shasta River confluence. A focus of this study was to improve what we believed to be negatively-biased estimates of escapement generated using redd counts. Unstratified Petersen carcass tag-recovery methods yielded 3.3 to 4.8 successfully spawned females per observed redd based on redd count data collected concurrently with carcass surveys. Based on Kimura-adjusted scale readings and unstratified Petersen escapement estimates, jacks (age-2 fish) represented less than 10% of the total annual escapement estimates for six of the ten survey years, with the greatest observed proportion of jacks occurring in 2006 (16%) and 2008 (17%). Low jack abundance in 2005 was indicative of low returns of age-3 adults in 2006 and age-4 adults in 2007 and similarly, low jack abundance in 2007 was indicative of low returns of age-3
adults in 2008 and age-4 adults in 2009. Despite low escapement estimates of adults in 2006, the abundance of jacks was relatively high, portending higher returns of 3-year old spawners in 2007 and 4-year old spawners in 2008. A similar pattern of low estimated escapement comprised of a relatively high abundance of jacks was observed in 2008, which was indicative of an abundance of 3-year old spawners in 2009 and 4-year old spawners in 2010. Pre-spawn mortalities of females ranged from about 22% in 2005 to 1% in 2009. Annual egg deposition by adult females calculated from unstratified Petersen estimates ranged from estimated highs of 24.5 and 25.0 million in 2002 and 2003, down to 5.7 and 4.7 million in 2006 and 2010.

Adult fall-run Chinook Salmon, escapement, Carcass Data, Tag Recovery
2012Thomas B. Hardy, Russell Perry, Sam Williamson, Thomas ShawApplication of a salmonid life cycle model for evaluation of alternative flow regimes., ,

The SALMOD Chinook (Oncorhynchus tshawytscha) life cycle model for the Klamath River, California, USA was updated to address a number of computational and life history limitations based on over 10 years of accumulated experience. SALMOD II incorporates a complete spatial delineation of each mesohabitat unit between Iron Gate Dam and the Klamath estuary (~320 km). Mesohabitat specific relationships for Chinook spawning, fry, presmolt and immature smolt life stages are based on site specific hydrodynamic modeling from 8 representative study sites that incorporate target mesohabitat characteristics of channel width and base flow magnitude. SALMOD II was calibrated and validated to multi-year collection data and incorporated improved density dependant movement and mortality factors, a disease factor, an improved water temperature simulation model and other key life history requirements. We explain the underlying computational framework for the modeling system, highlight the spatial delineation and extrapolation methodology for mesohabitat specific habitat versus flow relationships for each Chinook life stage, and highlight important factors such as emigration and density dependant habitat movement factors.

Chinook Salmon, Modeling
2009Scott Foott, Greg Stutzer, R. Fogerty, Hal Hansel, Steven Juhnke, John BeemanPilot study to access the role of Ceratomyxa shasta infection in mortality of fall-run Chinook smolts migrating through the lower Klamath River in 2008., 18010209

Apparent survival and migration rate of radio-tagged hatchery subyearling Chinook salmon released at Iron Gate Hatchery was monitored in the Klamath River to see if the timing of mortality coincided with observations of ceratomyxosis in re-captured coded wire tag cohorts. Despite rapid emigration, these relatively large (mean fork length 92 mm) smolts had a cumulative apparent survival to the estuary of 0.074 (SE 0.024) and standardized rates of survival per 100 km tended to decrease linearly with distance from the hatchery. The last fish detection occurred 26 days after release but median travel time between Iron Gate Hatchery (rkm 309) and the last receiver near the Klamath estuary (Blake’s Riffle rkm 13) was about 10 days. The majority of apparent mortality (8-10 d post-release) occurred before disease from Ceratomyxa shasta
infection is expected after exposure to infectious waters. Despite numerous observations of ceratomyxosis in the Klamath R. during June, an obvious link between disease and apparent survival was not present in this study. Future studies should examine the acute (e.g., predator types and densities) and chronic (e.g., swimming performance impairment due to disease) mortality factors for juvenile Chinook salmon smolts in the Klamath River.

Ceratomyxa shasta, mortality, Chinook smolts
2008John W. Beeman, Steve Juhnke, Greg Stutzer, Nicholas Hetrick, Survival and Migration Behavior of Juvenile Coho Salmon in the Klamath River Relative to Discharge at Iron Gate Dam, Northern California, 2007, , , 18010209

This report describes a study of survival and migration behavior of radio-tagged juvenile coho salmon (Oncorhynchus kisutch) in the Klamath River, northern California, in 2007. This was the third year of a multi-year study with the goal of determining the effects of discharge at Iron Gate Dam (IGD) on survival of juvenile coho salmon downstream. Survival and factors affecting survival were estimated in 2006 and 2007 after work in 2005 showed radio telemetry could be used effectively. The study has included collaborative efforts among U.S. Geological Survey (USGS), U.S. Fish and Wildlife Service (USFWS), the Karuk and Yurok Tribal Fisheries Departments, and the U.S. Bureau of Reclamation. The objectives of the study included: (1) estimating the survival of wild and hatchery juvenile coho salmon in the Klamath River downstream of Iron Gate Dam, determining the effects of discharge and other covariates on juvenile coho salmon survival (2) and migration (3), and (4) determining if fish from Iron Gate Hatchery (IGH) could be used as surrogates for the limited source of wild fish.

iron gate hatchery, coho salmon, tagging, disease
2014Mark Magneson, Philip ColombanoMainstem Klamath River Fall Chinook Salmon Redd Survey 2013, 180102

This report summarizes the 2013 fall Chinook salmon Oncorhynchus tshawytscha redd survey on the mainstem Klamath River and is the 21st such summary provided by the Arcata Fish and Wildlife Office. The survey was conducted over a 7-week period (October 22 to December 5, 2013), covering 114.7 river kilometers (rkm) between the Shasta River (rkm 288.5) and Indian Creek (rkm 173.8) confluences. We observed 2,611 fall Chinook salmon redds in 2013, which is the second highest count for this section of river since annual surveys began in 1993. Redd numbers over the previous 20-year history of this survey ranged from 243 (in 1993) to 3,390 (in 2012). The 2013 count is about 2.6 times larger than the prior 20-year mean (?? ? = 1,007). Redd densities within approximately 10-rkm sections were highest between China Creek (rkm 191.9) and Ottley Gulch (rkm 183.7; 60.4 redds/rkm) and lowest between Shasta River and Humbug Creek (rkm 279.7; 4.7 redds/rkm).

Chinook salmon, Klamath River, redd, escapement, spawning survey
2015Mark D. Magneson, Charles D. ChamberlainThe Influence of Lewiston Dam Releases on Water Temperatures of the Trinity River and Lower Klamath River, CA, April to October, 2014., , , 18010209

Water year 2014 was designated as “Critically Dry” in the Trinity River Basin, with 434,683 acre-feet of water released from Lewiston Dam to the Trinity River. This total water volume exceeded the Record of Decision prescribed volume of 369,000 acre-feet for a Critically DryWater Year due to additional releases made in the fall to reduce the risk of a fish kill occurring in the lower Klamath River. Water temperatures were monitored at several locations along the Trinity and lower Klamath rivers from April to mid-October 2014 to evaluate the influence of Lewistown Dam releases on downstream water temperatures. We compare observed values to water temperature objectives specified in the Trinity River Flow Evaluation Study and adopted by the Trinity River Record of Decision, including the spring-summer water temperature targets established for outmigrating salmonids and the objectives for the 64-kilometer reach located downstream of Lewiston Dam to protect holding and spawning adult salmonids. Additionally, we document the influence of Lewiston Dam releases on water temperatures in the lower Klamath River downstream of the confluence of the Trinity River and summarize data from 2002 to 2014 during the augmented fall flow period. This document is the thirteenth consecutive annual water temperature report generated for the Trinity River Restoration Program.

dam releases, Lewiston Dam
2006Mark Magneson, Stephen GoughMainstem Klamath River Coho Salmon Redd Surveys 2001 to 2005, 180102

Results of annual coho salmon Oncorhynchus kisutch redd surveys conducted on the mainstem Klamath River in November and December, 2001 through 2005 are summarized. The survey reach covers 136.5 river kilometers (rkm) located between Iron Gate Dam (IGD; rkm 310.3) near Hornbrook and the Indian Creek confluence at Happy Camp, California (rkm 173.8). A combined total of 38 coho salmon redds were observed within the survey reach for all five years combined. In 2001, eight additional redds were observed in the mainstem Klamath River downstream of the lower boundary of the study reach at Indian Creek. Within the survey reach, the highest annual redd count occurred in 2001 (n = 13). Seven redds were observed in 2003 and 6 redds were documented annually in 2002, 2004, and 2005. Coho salmon redds were observed in the mainstem Klamath River between November 15 and December 18, with the majority of new redds (63%) counted in mid December. About 68% of observed redds were located within 20 rkm of IGD and all redds were constructed within 1.5 rkm of a tributary mouth. Mean redd area (3.6 m2), mean pit depth (0.61 m), mean mound depth (0.38 m), mean adjacent depth (0.55 m), and focal velocity range (0.49-1.05 m/s) were greater than values reported in the literature for other systems, but sample sizes were too low for statistical comparison.

Redd Surveys, Coho Salmon
2006Charles D. Chamberlain, Samuel C. WilliamsonKlamath River Salmonid Emigrant Trapping Catch, Mortality, and External Health Indicators – 2004180102

Several field investigations conducted in spring and early summer of 2004 resulted in concurrent operation of young-of-year and age 1+ salmonid emigrant traps at six mainstem and three Klamath River tributary sites. Mortality sharply increased starting April 29 at the Bogus, I-5, and Kinsman frame trap sites. By early May, mortality approached 50% for wild young-of-year Chinook salmon captured at Kinsman, Happy Camp, and Persido Bar. From June 2 to June 18, mortality observed in daily catches of Chinook salmon at Kinsman ranged between 51% and 88%. Overall mortality of young-of-year Chinook salmon observed at lower mainstem trap sites (Persido Bar and Big Bar, 6% each) were paltry compared with those observed at Kinsman and Happy Camp (34% and 25%, respectively). In mid-May, a systematic external examination was incorporated into fish sampling as more than half of the live fish captured at Kinsman and Happy Camp exhibited external signs of disease and/or stress. High and low incidence of pale gills and other external abnormalities coincided with sites and time periods having high and low mortality. Based on external examinations, Kinsman was a “hotspot” of symptomatic young-of-year Chinook salmon (at 82%), declining downstream to Happy Camp (56%), Persido Bar (40%), and Big Bar (14%). Common external abnormalities noted in examinations of Chinook salmon included pale gills (pink or grey in color rather than a healthy red appearance), distended abdomen, gill rot, and lamprey wounds. Abnormality rates were highest at Kinsman and Happy Camp for all salmon species and age classes. Mortality was low at tributary traps operated at Horse Creek, Seiad Creek, and Elk Creek and captured fish were healthy in appearance. This agrees well with previous fish health investigations and two studies conducted on the Klamath River in 2004.

frame trap, mortality, fish health, abnormalities
2006Greg M. Stutzer, Jason Ogawa, Nicholas J. Hetrick, Tom ShawAn Initial Assessment of Radio Telemetry for Estimating Juvenile Coho Salmon Survival, Migration Behavior, and Habitat Use in Response to Iron Gate Dam Discharge on the Klamath River, California., , 18010209

High capture probabilities observed at automated radio telemetry arrays in 2005 indicate that radio telemetry should be a valid method for estimating survival of juvenile coho salmon in the Klamath River downstream from IGD. This technique has been used successfully to estimate survival of juvenile salmonids in the Columbia and Snake rivers for the last several years (Counihan et al. 2002, Skalski et al. 2002). One distinct advantage of radio telemetry over mark-recapture methods based on passive tags (PIT tags, coded-wire tags, T-bar anchor tags, fin clips, etc.) is the high capture probabilities possible with this method, which in turn reduces the number of tagged animals required.

iron gate dam, survival, migration behavior, habitat use, tagging
2006Thomas B. Hardy, Thomas Shaw, R. Craig Addley, Gary E. Smith, Michael Rode, Michael BelchikValidation of Chinook fry behavior‐based escape cover modeling in the lower Klamath River18010209

An emerging trend in the state-of-the-art instream flow assessment applications is the use of three-dimensional channel topography coupled with two-dimensional hydrodynamic models. These components are most often integrated with biological response functions for depth, velocity, and substrate to simulate physical habitat for target species and life stages. These approaches typically involve the simple extension of the one-dimensional conceptual habitat models represented by the Physical Habitat Simulation System (PHABSIM) developed by the U.S. Fish and Wildlife Service (Stalnaker, 1995). However, as demonstrated in this paper, the physical habitat based template represented by high-resolution channel topography and two-dimensional hydrodynamic model outputs can extend these simple conceptual models of habitat to incorporate additional behavior-based decision rules. The approach demonstrated in this paper evaluates the spatial suitability of physical habitat for chinook fry based on the incorporation of behavioral rule sets associated with instream object cover (i.e., velocity refuges) and in-water escape cover type and distance. Simulation results are compared to simplistic based physical habitat simulations using only depth, velocity, and substrate and validated against independent fish observation data. Results demonstrate that the functional relationship between predicted habitat and discharge utilized in many instream flow assessments is significantly different when the additional behavior-based decision rules are applied.

Chinook Salmon, modeling, chinook fry
2005Jefferson T. Hinke, George M. Watters, George W. Boehlert, Paul ZedonisOcean habitat use in autumn by Chinook salmon in coastal waters of Oregon and California

Describing the ocean habitats used by Chinook salmon Oncorhynchus tshawytscha is an important step towards understanding how environmental conditions influence their population dynamics. We used data from archival tags that recorded time, temperature and pressure (depth) to define the coastal habitats used by Chinook near Oregon and California during the autumns of 2000, 2002 and 2003. We used a clustering algorithm to summarize the data set from each year and identified 4 general habitats that described the set of ocean conditions used by Chinook. The 4 habitats, defined primarily by depth and the time of day that these depths were occupied, were characterized as (1) shallow day, (2) shallow night, (3) deep and (4) deepest. The definitions and use of each habitat were similar across years and the thermal characteristics of all habitats included water temperatures between 9 and 12°C. This temperature range provided the best indicator of Chinook habitat in the coastal ocean. Chinook used 9 to 12°C water at least 52% of the time. Less than 10% of surface waters within the area where Chinook were released and recovered provided these temperatures. Cross sections of subsurface temperatures suggest that between 25 and 37% of the coastal water column was available to Chinook and contained water in the 9 to 12°C range. These results support hypotheses that link salmon-population dynamics to ocean temperatures. Continued monitoring of surface and subsurface thermal habitats may be useful for assessing the extent and quality of conditions most likely to sustain Chinook salmon populations.
conditions most likely to sustain Chinook salmon populations.

Chinook Salmon, Ocean Habitat
1989D.V. Buchanan, A.R. Hemmingsen, D.L. Bottom, R.A. French, K.P. CurrensNative Trout Project: 1 October 1988 to 30 September 198918010203

Review available literature on the zoogeography and ecology of trout populations in the western United States and the implications for trout management. Review literature and historical accounts of the physical characteristics of native stream ecosystems and habitats in the region and changes in these conditions that have occurred since European settlement. Prepare a standard survey for interviewing Oregon Department of Fish and Wildlife (ODFW) biologists and other resource professionals to evaluate management objectives and review the current status of inventory information for native trout populations and their habitats.

Redband trout, Native trout
1991L.A. BorgersonScale Analysis: October 1, 1989 to September 30, 1991,

This report identifies the rearing origin of coho salmon (wild, hatchery yearling, or hatchery accelerated) spawning in Oregon coastal streams and at hatchery broodstock collection facilities. Determine the age composition and length at age of chinook salmon in Oregon coastal index streams. Determine the age composition and early life history of spring and fall races of chinook salmon in the Rogue River. Determine the age composition of chum salmon spawning in Tillamook Bay and Nestucca River tributaries. Determine the age of maturity, spawning history, and growth rates of native redband trout. Determine the length at age, age frequency, and changes in growth rates of largemouth and smallmouth bass sampled in Oregon rivers, lakes, and reservoirs.

scale analysis
1992L.A. BorgersonScale Analysis Annual Progress Report: October 1, 1991 to September 30, 1992, ,

This report identifies the rearing origin of coho salmon (wild, hatchery yearling, or hatchery accelerated) spawning in Oregon coastal streams and at hatchery broodstock collection facilities. Determine the age composition and length at age of chinook salmon in Oregon coastal index streams. Determine the age composition of chum salmon spawning in Tillamook Bay and Nestucca River tributaries. Provide scale analysis support to other research and management projects. Maintain scale archives.

scale analysis
1984Jean M. Beyer Rainbow trout fishery and spawning stock in the Upper Klamath River Wild Trout Area, Copco, California, 18010203

The rainbow trout fishery in the Upper Klamath River Wild Trout Area was examined in 1981 and 1982. In the spring of 1982, 281 mature rainbow trout were trapped at the mouth of Shovel Creek, the only known spawning tributary to the area. Males were 78 percent age two and females were 89 percent age three. Less than 10 percent of the upstream migrants had scale checks indicating prior spawning and less than 10 percent were recaptured as spent downstream migrants. Spawning success could have been limited by a lack of suitable spawning gravel, dewatering of redds from irrigation diversions, and fine sediments in the redds (13 percent of redd volume less than 0.85 millimeters in diameter) possibly from logging and cattle grazing in the area. The 1982 spawning produced a year class estimated to contribute a maximum of 32,903 fish to the Upper Klamath River. Most emigrated at age 0, and the few older fish rearing in Shovel Creek had slower growth than spawners or creeled fish. Rainbow trout creeled in the Upper Klamath River Wild Trout Area were primarily age one and two, with yearlings entering the fishery in late July. Creeled fish were significantly larger than spawners at back-calculated ages one (p < 0. 05) and two (p <0.01). Catch averaged 0.5 rainbow trout per hour; average fork length was 240 millimeters. Juvenile steelhead stoced in Copco Reservoir (31,000 to 100,312 yearly in 1978 to 1980) possibly contributed to the Upper Klamath River Wild Trout Area creel and/or the Shovel Creek spawning run.

Redband trout, spawning stock
2015William R. Tinniswood, Michael HarringtonLife History and Monitoring of Upper Klamath-Agency Lakes Adfluvial Redband Trout, 18010203

Spawning surveys are the primary monitoring tool for monitoring bull trout and anadromous fish species in Oregon (Jacobs et al. 2009, Gallagher et al. 2007, Jacobsen et al. 2014,). Randomized redd counts are utilized to monitor steelhead escapement on coastal Oregon tributaries (Jacobsen et al. 2014).

Numerous studies of disparate salmonid species have shown positive significant relationships between redd counts and estimates of escapement (Gallagher et al. 2007), redd counts are strongly correlated with adult escapements (Dunham et al. 2001) and bull trout redd counts can detect a 50% decline in the population over 10 years (Howell and Sankovich 2012). However, redd counts can have significant sources of bias and error (Dunham et al. 2001), 5 year trends in redd counts can be misleading (Howell and Sankovich 2012) and redd counts should be conducted by experienced surveyors (Howell and Sankovich 2012, Muhlfield et al. 2006).

Redband trout, monitoring, bull trout, anadromous fish
2010William R. Tinniswood, Mary Buckman, Ariel C. MuldoonStatistical Creel Survey on Upper Klamath and Agency Lakes in 2009 and 2010, 18010203

A roving type statistical creel survey was performed in Upper Klamath and Agency Lakes in the years 2009 and 2010 during the peak months of angling effort from March-September. Pressure counts and angler interviews were conducted to determine catch, harvest, and catch per unit effort of the trophy redband trout fishery. The purpose of the survey was to collect information to evaluate potential management changes that have been proposed by the public during multiple Sport Fish Regulation meetings. Overall catch rates were similar in 2009 and 2010. Average catch rates for all anglers in 2009 was 0.11 redband trout/hour (9 hours per redband trout) and 0.10 redband trout/hour (10 hours per redband trout). However, boat anglers had much higher catch rates (range: 3.6-8.5 hours per redband trout) than bank anglers (range: 21-58.8 hours per redband trout). Bank angling at Agency Lake during the spring of 2010 was the lowest catch rate ever recorded (58.8 hours per redband trout) while boat angling on Agency Lake during the summer had the highest catch rate ever recorded (3.6 hours per fish). Most redband trout captured in the fishery were released (88% in 2010 and 83% in 2009) with an estimated 729 harvested in 2010 and 943 harvested in 2009 (Total fishery removal 1582 and 1772). Angler effort was estimated at 49,695 hours in 2010 and 57,769 hours in 2009. Average size of redband trout captured in the fishery was 517 mm (20.35 inches). Anglers harvested larger redband trout than average (544 mm, 21.4 inches fork length). Management implications for the future should consider the high catch rate during the summer in Agency Lake and Pelican Bay Area. Water temperatures at the surface can reach 28° C during the summer where redband trout are caught and subsequently released. Gear restrictions might be considered. High catch and release rates were observed by anglers still fishing with worms in Pelican Bay during the summer which can lead to mortality exceeding 20%.

Redband trout
2007R. Kirk Schroeder, James D. HallRedband Trout Resilience and Challenge in a changing landscape, , ,

In September 1996, 85 redband trout enthusiasts gathered at the Malheur Field Station in Harney County, Oregon for a workshop sponsored by the Oregon Chapter of the American Fisheries Society. All of us gathered to talk about the biology and status of redband trout, and to share our appreciation for this diverse fish. Concern about redband trout had been building in the region because of continued drought and the apparent decline of some populations, including the disappearance of redband trout in some streams such as Skull Creek in the Catlow Valley (Howell 1997). The status of redband trout throughout its range was considered to be precarious enough that it had been classified by the U.S. Fish and Wildlife Service as a candidate for being listed as an endangered species, though lack of information about its status or other factors had precluded listing.

Thirteen papers from the 1996 workshop are included in these proceedings. Most of them have been revised and updated to include recent data or to report on changes in management. Two additional papers that were not in the workshop have been included because we felt they would complement the other papers. It is our hope that these proceedings will provide a useful resource for those working with or interested in redband trout. Although the workshop used the term “inland rainbow trout” to describe populations of Oncorhynchus mykiss in the Columbia Basin east of the Cascade Mountains and those of the Northern Great Basin (including the Upper Klamath Lake Basin), we choose to use “redband trout” for these proceedings, following Behnke (1992, 2002). One theme that runs through these papers is the tremendous diversity expressed by redband trout; from the habitats they inhabit (ranging from cold mountain rivers to high desert streams) to their diverse life histories that have allowed them to adapt to a wide range of environmental conditions.

Evolutionary Diversity, Genetic Analysis, Endangered Species Act
2007Rhine T. Messmer, Roger C. SmithAdaptive Management for Klamath Lake Redband Trout, 18010203

The upper Klamath River basin trout fishery consistently produces redband trout Oncorhynchus mykiss that exceed 4.5 kg. It is among the finest trout fisheries in the United States. The redband trout of the upper Klamath River basin have evolved in harsh environmental conditions and may be uniquely adapted to the habitats found in Upper Klamath and Agency lakes. These redband trout also have developed behavioral and life history characteristics that enable them to inhabit the highly eutrophic waters of the Klamath Basin. The management of Klamath Lake redband trout has evolved from the early 1920s, when large numbers of hatchery trout were stocked to supplement consumptive recreational fisheries, to the 1990s, when natural production, habitat protection and enhancement, and conservative angling regulations were used to provide for trophy redband trout fisheries. This evolution in management resulted from evaluating hatchery trout stocking programs and collecting information on stock-specific disease resistance, life history, and genetics. In addition, changes were made in Oregon Department of Fish and Wildlife trout management policies that emphasized the importance of native fish. Fish managers should continue to collect new information critical for sound, biologically based management of redband trout, and to incorporate this information into management plans.

Redband trout, adaptive management
2016Interior Redband Conservation TeamConservation Strategy for Interior Redband (Oncorhynchus mykiss subsp.) in the States of California, Idaho, Montana, Nevada, Oregon and Washington

This document provides goals and objectives for Redband conservation across its range, and specific stepwise goals, objectives and actions for each of the eight Redband Geographic Management Units (GMUs). When implemented, these measures significantly address the needed conservation efforts described above. As described in some of the GMU sections of this document, before specific conservation actions can be prescribed, additional sampling is needed to characterize the genetic status of these populations.

conservation, redband trout
2002A. Kurt Gamperl, Kenneth J. Rodnick, Heather A. Faust, Emilee C. Venn, Max T. Bennett, Larry I. Crawshaw, Ernest R. Keeley, Madison S. Powell, Hiram W. LiMetabolism, Swimming Performance, and Tissue Biochemistry of High Desert Redband Trout (Oncorhynchus mykiss ssp.): Evidence for Phenotypic Differences in Physiological Function,

Redband trout (Oncorhynchus mykiss ssp.) in southeastern Oregon inhabit high-elevation streams that exhibit extreme variability in seasonal flow and diel water temperature. Given the strong influence and potential limitations exerted by temperature on fish physiology, we were interested in how acute temperature change and thermal history influenced the physiological capabilities and biochemical characteristics of these trout. To this end, we studied wild redband trout inhabiting two streams with different thermal profiles by measuring (1) critical swimming speed (Ucrit) and oxygen consumption in the field at 12 and 24C; (2) biochemical indices of energy metabolism in the heart, axial white skeletal muscle, and blood; and (3) temperature preference in a laboratory thermal gradient. Further, we also examined genetic and morphological characteristics of fish from these two streams.

Redband trout, metabolism,
2009Kenneth P. Currens, Carl B. Schreck, Hiram W. LiEvolutionary Ecology of Redband Trout

We examined genetic differences at 29 enzyme encoding loci among 10,541 rainbow trout Oncorhynchus mykiss from 240 collections throughout the species’ range, including redband trout (i.e., several rainbow trout subspecies) in pluvial lake basins of the northern Great Basin that have had largely internal drainage with no connection to the Pacific Ocean. Differences among groups accounted for 29.2% of the genetic variation. Although we observed major genetic differences between coastal and inland groups (10.7%), which are currently considered to represent the major phylogenetic division in the species, we found that the greatest evolutionary divergence (19.7%) was related to persistence of three major river systems: the upper Sacramento, Klamath, and Columbia rivers. Genetic traits of redband trout from the northern Great Basin, where we found distinct subspecies or races, indicated that over millennia these pluvial habitats were sources of evolutionary diversity associated with large river systems rather than completely isolated refugia. However, redband trout did not constitute a distinct monophyletic group. Based on our data, redband trout of the Goose Lake, Warner Valley, and Chewaucan basins were distinct genetic races that were part of the diverse complex of Sacramento redband trout O. mykiss stonei. Harney Basin redband trout were a unique genetic race most closely associated with Columbia River redband trout O. mykiss gairdneri. White River and Fort Rock redband trout were associated with the Columbia River but showed allelic divergence comparable with that among other subspecies. Upper Klamath Lake rainbow trout included a previously unrecognized group associated with populations in the headwaters of the basin and a different subspecies from type locations for Upper Klamath Lake redband trout O. mykiss newberrii (i.e., Upper Klamath Lake and the upper Klamath River).

Redband trout, evolutionary ecology
2005R. Craig Addley, Bill Bradford, Jennifer LudlowKlamath River Bioenergetics Report, , , 180102

The results of the bioenergetics foraging model and P value model indicate that food availability is more important than water temperature as a factor in trout growth in the J.C. Boyle peaking reach for the Existing Conditions, WOP and Steady Flow scenarios. There is relatively little difference in four-year growth predictions between Existing Conditions, Steady Flow, and WOP scenarios in the J.C. Boyle peaking reach when only changes in water temperature were incorporated into the modeling. This happened because there was only a relatively small difference in daily temperatures between the three scenarios relative to the temperature-related growth requirements of trout. The biggest effect on predicted growth came from the assumption that increased invertebrate drift/ food availability would occur under the WOP and Steady Flow scenarios. The most uncertainty exists in this parameter, however. Based on the literature, food would likely increase, but the amount is uncertain. The invertebrate drift densities observed below Iron Gate dam or in the Keno reach provide a reasonable upper bound on the increase that could occur in the J.C. Boyle peaking reach. Actual drift density for the WOP and Steady Flow scenarios may be somewhere between what they are now with Existing Conditions and this upper bound.

Bioenergetics
2017National Fish and Wildlife Fund (NFWF) National Fish and Wildlife Fund (NFWF) grants page,

The National Fish and Wildlife Fund (NFWF) provides funding on a competitive basis to projects that sustain, restore, and enhance our nation's fish, wildlife, and plants and their habitats.

Each of our initiatives has a business plan developed by scientists and other experts and approved by our Board of Directors. Grants are available to support the actions identified in the business plan. Additional programs support diverse projects for wildlife and habitat conservation across the country.

Search the grants library for descriptions, interim reports, photos, and final reports of their grants in the Klamath Basin.

conservation
2010ODFWStatus Klamath Rainbow/Rainbow Trout Dams in Scenario. Klamath River Rainbow Trout Peaking Reach Klamath River, , , 180102

The purpose of this document is to provide an outline for a presentation by ODFW staff to the expert panel on redband, rainbow and bull trout which will provide input for the secretarial determination of whether to remove the four hydroelectric dams on the Klamath River. The expert panel will evaluate if the continued operation of the four main stem hydro electric facilities is in the best interest of the people of the United States and if fisheries will benefit.

Redband trout, rainbow trout, bull trout
2005ODFWUpper Klamath Basin Redband Trout SMU18010206

The Upper Klamath Lake basin contains the remnants of Pleistocene Lake Modoc, which redband trout may have entered from interior connections. Currently, the Upper Klamath Lake Basin supports the largest and most functional adfluvial redband trout populations of Oregon interior basins, however, some populations are severely limited in distribution and abundance by habitat quality and non-native species. The SMU is comprised of 10 populations that vary in life history, genetics, disease resistance, and status. Eighty percent of the populations meet three of the six interim criteria, thereby classifying this SMU as ‘at risk’. Limited data sets and inferences from other information for populations in this SMU provide a qualified level of confidence in the assessment of the interim criteria.

Redband trout
2005ODFWUpper Klamath Basin Redband Trout18010206

The Upper Klamath Lake basin contains the remnants of Pleistocene Lake Modoc, which redband trout may have entered from interior connections. Currently, the Upper Klamath Lake basin supports the largest and most functional adfluvial redband trout populations of Oregon interior basins, however, some populations are severely limited in distribution and abundance by habitat quality and non-native species. The SMU is comprised of ten populations that vary in life history, genetics, disease resistance, and status. Eighty percent of the populations meet three of the six interim criteria, thereby classifying this SMU as 'at risk'. Limited data sets and inferences from other information for populations in this SMU provide a qualified level of confidence in the assessment of the interim criteria.

Redband trout
2015Clint C. Muhlfeld, Shannon E. Albeke, Stephanie L. Gunckel, Benjamin J. Writer, Bradley B. Shepard, Bruce E. MayStatus and Conservation of Interior Redband Trout in the Western United States

In this article we describe the current status and conservation of interior (potamodromous) Redband Trout Oncorhynchus mykiss sspp. throughout its range in the western United States using extant data and expert opinion provided by fish managers. Redband Trout historically occupied 60,295 km of stream habitat and 152 natural lakes. Currently, Redband Trout occupy 25,417 km of stream habitat (42% of their historical range) and 124 lakes or reservoirs. Nonhybridized populations are assumed to occupy 11,695 km (46%) of currently occupied streams; however, fish from only 4,473 km (18%) have been genetically tested. Approximately 47% of the streams occupied by Redband Trout occur on private land, 45% on government lands, and 8% in protected areas. A total of 210 Redband Trout populations, occupying 15,252 km of stream habitat (60% of the current distribution) and 95,158 ha of lake habitat (52%), are being managed as “conservation populations.” Most conservation populations have been designated as weakly to strongly connected metapopulations (125; 60%) and occupy much more stream length (14,112 km; 93%) than isolated conservation populations (1,141 km; 7%). The primary threats to Redband Trout include invasive species, habitat degradation and fragmentation, and climate change. Although the historical distribution of interior Redband Trout has declined dramatically, we conclude that the species is not currently at imminent risk of extinction because it is still widely distributed with many populations isolated by physical barriers and active conservation efforts are occurring for many populations. However, the hybridization status of many populations has not been well quantified, and introgression may be more prevalent than documented here.

Redband trout, conservation, status
2006Steven E. Jacobs, Steven J. Starcevich, William TinniswoodEffects of Impoundments and Hydroelectric Facilities on the Movement and Life History of Redband Trout in the Upper Klamath River: A Summary and Synthesis of Past and Recent Studies, 18010206

The physical and ecological environment of redband trout in the Upper Klamath River has been altered by hydroelectric dams. Four dams and five distinct river reaches are currently present in the 48-mile section between the outflow of Upper Klamath Lake and the Oregon- California Border. Spencer Creek, which enters the Klamath River just upstream of J.C. Boyle Dam, is an important spawning area and source of juvenile recruitment for redband trout in the upper Klamath River. In 1959, the year after J.C. Boyle Dam was completed, fish ladder trap counts showed adult redband trout migrated upstream in the Klamath River in large numbers to spawn in Spencer Creek. By 1962, trap counts had declined by at least 90%. Despite this decline, studies conducted in the late 1980s showed that a significant spawning run and juvenile outmigration persisted in Spencer Creek. These findings left questions about the adult and juvenile life history of Spencer Creek spawning population. We used radio telemetry and PITtag technology to address these questions. Our results suggest that, since the construction of J. C. Boyle Dam, upstream movement of adult redband trout to Spencer Creek has been eliminated and movement of juveniles from Spencer Creek downstream past the dam has been restricted to periods when spill occurs. We also found that the Keno Reach of the Klamath River is the main source of spawning adults in Spencer Creek. In total, these results suggest that diversity of life histories displayed by Spencer Creek spawners has been constricted by the construction of J.C. Boyle Dam This reduction in life history diversity has likely reduced trout abundance downstream of the dam. These results also show that the extant adult life history is composed of a downstream spawning migration in Klamath River to Spencer Creek and a substantial juvenile upstream migration to the Keno Reach.

Redband trout, Impoundments, Hydroelectric Facilities
2006Richard W. Stocking, Richard, A. Holt, J. Scott Foott, Jerri L BartholomewSpatial and Temporal Occurrence of the Salmonid Parasite Ceratomyxa shasta in the Oregon–California Klamath River Basin, 180102

The parasite Ceratomyxa shasta has been implicated as a significant source of salmonid mortality in the lower Klamath River, California (i.e., below Iron Gate dam). A study of the prevalence of C. shasta and its geographic and temporal distribution throughout the Klamath River basin was conducted to determine when and where juvenile salmonids encounter lethal parasite doses. Susceptible rainbow trout Oncorhynchus mykiss were exposed to C. shasta 3–4 d at seven locations in the Klamath River between Beaver Creek and Keno Reservoir in April, June, July, September, and November 2003. Individuals from a Klamath River strain of fall Chinook salmon O. tshawytscha were held in three locations in the upper Klamath River in April, June, and July. In June 2004, rainbow trout were exposed to the parasite for 4 d at 18 locations from Klamath Lake to the mouth of the Klamath River, including several major spawning tributaries; one exposure occurred in the lower Klamath River. Rainbow trout mortality due to infection for groups exposed in the upper Klamath River was lower (,8.0%) and delayed (mean time to death, 40–110 d) in comparison with that in groups exposed in the lower Klamath River (.98%; mean time to death, 33–36 d). Experimental fall Chinook salmon did not become infected in the upper Klamath River, but infection was detected in Chinook salmon exposed in the lower Klamath River, nearly 50% of these succumbing to infection. These dramatic differences in mortality between the upper and lower Klamath River could not be explained by differences in water temperatures during exposure and are probably a result of differences in infectious dose. Lack of infection in groups exposed in tributaries supports the hypothesis that the parasite life cycle and the invertebrate host are largely confined to the main-stem Klamath River.

parasite, Ceratomyxa shasta
2006ODFWPreliminary comments and 10(J) Recommended terms and conditions for Pacificorp’s Klamath Hydroelectric Project, , , , 180102

This document provides the Oregon Department of Fish and Wildlife’s (ODFW) Section 10(j) Recommended Terms, and Conditions for relicensing of PacifiCorp’s relicensing of the Klamath Hydroelectric Project (Project) Federal Energy Regulatory Commission (FERC) Project No. 2082. Our comments are organized first with a section describing the authorities that guide ODFW’s participation in this relicensing process, followed by comments and recommended terms and conditions for the new license for operation of the Project. These terms and conditions may be modified as needed with the issuance of the FERC Draft Environmental Impact Statement, and as new information and additional study reports from the Licensee, federal, state and tribal entities are made available during the remainder of the relicensing process.

ODFW, FLA, relicensing
2006Thomas H. Williams, Eric P. Bjorkstedt, Walt G. Duffy, Dave Hillemeier, George Kautsky, Tom E. Lisle, Mike McCain, Mike Rode, R. Glenn Szerlong, Robert S. Schick, Matthew N. Goslin, Aditya AgrawalHistorical Population Structure of Coho Salmon in the Southern Oregon/Northern California Coasts Evolutionary Significant Unit, 180102

The main purpose of technical recovery planning for Pacific salmon and steelhead is to produce biologically based viability criteria for listed Evolutionarily Significant Units (ESUs) that will be considered in setting recovery goals. These viability criteria, and the analyses from which they stem, must refer to specific populations and population groups (i.e., populations or groups of populations within a ESU). The purpose of this report is to describe the historical population structure of coho salmon in the Southern Oregon/Northern California Coast (SONCC) ESU in order to guide viability analyses, and to provide a historical context for other parties interested in recovering coho salmon in the geographic region. We collected and examined available information relevant to the question of population structure of coho salmon in the SONCC ESU, and we present that information here.

SONCC, historical populations, coho salmon, air temperature
2016California Department of Fish and WildlifeKlamath River Cooperative Spawner Survey Overview Report, 180102

The middle Klamath Cooperative Spawning Ground Surveys (SGS) originated in 1986 and were originally funded by the Klamath River Basin Conservation Area Restoration Program (the Klamath Act) as part of a comprehensive plan to restore anadromous fish in the Klamath Basin. Federal legislation supporting the Klamath Act expired in 2006 and was not reauthorized by Congress. Since that time the U.S. Fish and Wildlife Service has continued to contribute substantial funding to the SGS effort using discretionary funding from their annual budget. The SGS collect data annually on Klamath River Fall Chinook (KRFC) spawning in natural areas for fishery management purposes. SGS cooperators include the U.S. Forest Service, U.S. Fish and Wildlife Service, Yurok Tribe, Karuk Tribe, Quartz Valley Tribe, Northern California Resource Center, Siskiyou Resource Conservation District, Mid-Klamath Watershed Council, Salmon River Restoration Council, the California Department of Fish and Wildlife and local schools and volunteers.

This report describes the areas surveyed by the SGS and how the data are generally obtained and applied in the annual management of KRFC.

Chinook Salmon, fall chinook run, spawning success, Klamath Tributaries, Klamath Mainstem, SGS
2013NOAAInstream Candidate Actions Table Mid Klamath Master Spreadsheet, , , , , , , , 180102

Instream Candidate Actions Table Mid Klamath Master Spreadsheet of applicable goals and objectives, action types, current projects, proposed projects, specific project to be accomplished and comments and other species concerns.

Coho salmon, fish passage, floodplain connectivity
2016Steven Stenhouse, Rosa Albanese and William R. ChesneyThree Year Report 2013-2015 Shasta and Scott River Juvenile Salmonid Outmigrant Study, , , , 18010209

Since 2000, the Anadromous Fisheries Resource Assessment and Monitoring Program (AFRAMP) conducted by the Yreka office of the California Department of Fish and Wildlife has operated rotary screw traps in the Scott and Shasta Rivers of the greater mid-Klamath River basin for the purpose of generating population estimates for out-migrating juvenile salmon. Described here are the results obtained during the 2013-2015 sampling seasons. Using rotary screw traps, all age classes of outmigrating Chinook salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch), and steelhead trout (O. mykiss), as well as a variety of native and non native fish species were sampled over these three years. Only Chinook and coho salmon data will be presented in this report. Using the Carlson method for mark and recapture of salmonids, trap efficiencies and population estimates were produced on a weekly basis. Established age-length cutoffs for each species were used to determine fish age. In-stream conditions such as flow and water temperature were also monitored. Weekly estimates for the smolt class of all species were compared to show multi-year population trends. Using multi-year seasonal production estimates and coho salmon returns to the Shasta River, adult survival and smolt production estimates were calculated for Shasta River coho. In 2013, it was estimated a total of 5,218,270 0+ Chinook, 1,930 0+ coho, and 494 1+ coho emigrated from the Shasta River during the sampling period. It was also estimated for the same sample period that 656,031 0+ Chinook, 1,290 0+ coho, and 7,927 1+ coho emigrated from the Scott River. In 2014, a total of 4,744,838 0+ Chinook, 10,752 0+ coho, and 850 1+ coho emigrated from the Shasta River. Additionally, 423,085 0+ Chinook, 760 1+ Chinook, 16,962 0+ coho, and 5,708 1+ coho, emigrated from the Scott River. It was estimated that for the period sampled in 2015, a total of 2,901,966 0+ Chinook, 851 0+ coho, and 6,279 1+ coho emigrated from the Shasta River.

Bio-sampling, Age Determination, Trap Efficiency
2016Christopher Adams and Caitlin BeanShasta River Brood Year 2012 Juvenile Coho Salmon PIT Tagging Study, 18010209

This report summarizes PIT tag data collected on brood year 2012 coho in the Shasta River (the progeny of adult coho that spawned in 2012). The key findings of this study were: 1. Overall known survival of PIT tagged BY2012 coho, from the time they were tagged in upper Shasta River in 2013 to outmigration into the Klamath River in the spring of 2014, was 33%. 2. Over 70% of the coho fry tagged in the upper Shasta River downstream of Big Springs Creek migrated upstream in May and June 2013 when stream temperatures increased to ~20 C. 3. Coho utilized a small spring complex adjacent to the Shasta River downstream of Parks Creek as short term thermal refugia during May and June 2013. 4. Successful summer rearing occurred in areas with cold spring inflows, including Little Springs Creek. 5. Overall, known survival was lowest during winter with the poorest winter survival occurring in Big Springs Creek. 6. Outmigrating coho smolts that were known to be alive in the upper Shasta River in March 2014 survived to reach the Klamath River at a rate of 90%, which is higher than documented in the BY2010 study (77%).

coho, coho salmon, Shasta River
2016California Department of Fish and WildlifeShasta River Brood Year 2013 Juvenile Coho Salmon PIT Tagging Study18010209

This report summarizes passive integrated transponder (PIT) tag data collected on brood year 2013 (BY2013) juvenile coho in the Shasta River (the progeny of adult coho that spawned in 2013). The key findings of this study were: 1. Overall known survival of the 647 BY2013 PIT tagged coho, from the time they were tagged in the upper Shasta River in 2014, to outmigration into the Klamath River in the spring of 2015 was
22%. 2. Four percent (n=27) of the BY2013 coho PIT tagged in the upper Shasta River outmigrated between May 26 and June 26 in 2014. Based on their size and appearance, we consider these fish to be age-0 smolts.
3. During residency in the Shasta River, overall seasonal survival of PIT tagged juvenile coho in the upper Shasta River was similar from season to season, ranging from 61% in the summer to 72% in the winter.
4. Known summer survival of 144 PIT tagged juvenile coho relocated from Parks Creek to Kettle Spring (67%) was similar to known summer survival of 49 tagged coho that were naturally occurring in Kettle Spring (71%). This was higher than known summer survival of 22 coho tagged and released in Parks Creek without being relocated (9%), likely due to habitat conditions. 5. Known survival of age-1 smolts encountered in February 2015 (or later) and then again at RKM 1 as they outmigrated to the Klamath River was 67%. This is lower than smolt survival to outmigration documented in the BY2010 study (77%) and the BY2012 study (91%).

coho, coho salmon, Shasta River
2016California Department of Fish and WildlifeScott River Brood Year 2013 Juvenile Coho Salmon PIT Tagging Study18010209

Extremely low flow conditions occurred in the Scott River watershed during the summer and fall of 2013 and 2014, due to the combined effects of drought and irrigation water withdraws. Low flows and disconnected
tributaries limited the extent of upstream migration of a relatively large adult coho return (n=~2,731) in 2013. Most spawning occurred in the mainstem Scott River rather than in the tributaries where it is more commonly
documented. This resulted in a situation where large numbers of juvenile coho were likely to be subject to high mortality rates in drying reaches of the Scott River. The California Department of Fish and Wildlife (CDFW), in
collaboration with other organizations, agencies and landowners undertook a fish relocation effort to remove juvenile salmonids from drying sections of the Scott River and place them in other locations in an attempt to
reduce the rate of mortality. Based on snorkel survey observations, over 118,250 juvenile coho were estimated to be present in the mainstem Scott River between Etna Creek and the Fay Lane Bridge in May 2014. An estimated 115,999 juvenile coho were relocated from the Scott River mainstem to tributary locations. A total of 1,872 of the relocated coho were implanted with passive integrated transponder (PIT) tags and CDFW operated six instream PIT tag detection stations in the watershed to evaluate the movements and survival of PIT tagged fish. A sample of 1,423 juvenile coho were also PIT tagged and released at the point of capture (981 were PIT tagged prior to September 1, 2014 and 442 were PIT tagged on September 1, 2014 or later) so that we could compare movements and survival between tagged fish that were relocated and those that were not. In addition, a total of 4,447 juvenile coho were taken to Iron Gate Hatchery (IGH) to rear in circulating round tanks. Of those fish, 390 were PIT tagged. These fish were returned to the mainstem Scott River and French Creek in October 2014.

coho salmon, coho, Scott River
2016California Department of Fish and WildifeLittle Shasta River-A Compendium of Available Information, , , 18010209

The purpose of this document is to provide information regarding the historical and current conditions of the Little Shasta River, tributary to the Shasta River, in Siskiyou County, California. The Shasta River watershed provides spawning and rearing habitat for three salmonid species; Chinook salmon, coho salmon, and steelhead. At one time, the Little Shasta River provided high quality aquatic habitat. However, under current conditions it has elevated water temperatures and goes dry in the summer in the 11-mile-long valley reach. With the listing of coho salmon under both the California and federal endangered species acts it has become a high priority to identify restoration activities that will enhance coho recovery in the watershed and improve habitat conditions for other aquatic species as well. We thought it was important to gather all the historic information available to determine how this watershed once functioned. In addition, Department of Fish and Wildlife personnel collected water temperature data over a two-year period to assess the potential for the upper watershed to provide over summering habitat for salmonids. The various pieces of information presented here will inform the question: “what steps would be necessary to restore the Little Shasta River to functioning salmonid habitat?” We do not explicitly answer that question. It is our hope that this information will help land-owners and decision-makers come up with that answer.

Shasta, coho, Chinook, steelhead
2013Ann Willis, Andrew Nicholas, Carson Jeffres, Mike DeasWater Resources Management Planning: Conceptual Framework and Case Study of the Shasta Basin, , , , , 18010209

northern California. Historically, the Shasta River was one of the most productive salmon streams in California. Cold and nutrient-rich groundwater springs provided nearly ideal aquatic habitat conditions supportive of large Chinook and coho salmon populations. However, more than a century of aquatic and riparian habitat degradation along the Shasta River and its tributaries has resulted in dramatic declines in wild salmon populations, and particularly the federally threatened coho salmon. Elevated water temperature is the primary factor limiting coho abundance in the Shasta River, and restoration of cold-water flows is the key to coho population recovery. The observed decline of coho in the Shasta River coincided with the development of surface and groundwater sources in support of irrigated agricultural activities throughout the Shasta Basin. Water development led to reductions in the quantity and quality of cold-water habitats required by rearing coho salmon. Developing a collaborative approach to water resource management is critical to both recovering coho salmon and maintaining a viable agricultural community with the Shasta Basin – without involving all stakeholders, successful solutions cannot be developed for either user group. Key to such an approach is the generation of a comprehensive water resources management plan that identifies collaborative solutions to providing water of suitable quantity and quality, at the appropriate place and time, such that the water needs of both the aquatic ecosystem and agricultural community are met.

Chinook, coho, water temperature, water quantity
2011Devon E. Pearse , Stephanie L. Gunckel, & Steven E. JacobsPopulation Structure and Genetic Divergence of Coastal Rainbow and Redband Trout in the Upper Klamath Basin, 18010206

Freshwater-resident coastal rainbow trout Oncorhynchus mykiss irideus and the anadromous form of the subspecies, coastal steelhead (summer and winter runs), are present throughout the lower Klamath River–Trinity River system. Although coastal steelhead and other anadromous salmonids historically migrated into the Upper Klamath Basin (which encompasses the upper Klamath River and Upper Klamath Lake) and associated tributaries, the construction of Copco Dam in 1918 and Iron Gate Dam in 1962 stopped all upstream migration of fish past these barriers. In the Upper Klamath Lake basin, native Upper Klamath Lake redband trout O. mykiss newberrii are found along with coastal rainbow trout that were trapped above the dams or stocked from hatchery sources. However, relatively little is known about the genetic relationships among the O. mykiss populations within the Upper Klamath Basin. A population genetic analysis based on data from 17 variable microsatellite loci was conducted for samples collected in the Upper Klamath Basin, including rainbow trout and Upper Klamath Lake redband trout (presumably representative of the ancestral coastal and inland lineages) as well as samples of O. mykiss from neighboring inland lake basins. In addition, the Upper Klamath Basin samples were compared with data from O. mykiss populations below Iron Gate Dam. Results demonstrate the presence of distinct inland and coastal genetic lineages as well as divergent lineages represented by samples from the inland lake basins; these results have significant implications for future restoration of O. mykiss in the greater Klamath River–Trinity River system.

redband trout, rainbow trout, steelhead
2016Steven A. Stenhouse, Amy J. Debrick and William R. ChesneyScott and Shasta River Juvenile Chinook Salmon Out-Migrant Study, 18010209

Since 2000, the Anadromous Fisheries Resource Assessment and Monitoring Program conducted by the Yreka office of the California Department of Fish and Wildlife has operated rotary screw traps in the Scott and Shasta
Rivers of the greater mid-Klamath River basin for the purpose of generating population estimates for out-migrating juvenile salmon. The traps are installed in late winter (Julian week 5 – January 29) and operate until late spring (Julian week 26 – July 1), depending on conditions. Three species of salmonid are monitored, including Chinook salmon (Onchorhynchus tshawytscha), coho salmon (O. kisutch) and rainbow trout/steelhead (O. mykiss), as well as a variety of native and non-native fish species. This report is a summary of data collected regarding juvenile Chinook populations from 2000 to 2015. Seasonal population estimates at the Scott River trap site ranged from 17,000 in 2006 to a high of 1,190,000 fish in 2009. Production estimates from the Shasta River ranged from 90,000 in 2006 to 5,975,000 individuals in 2013. Out-migration timing, estimated trap efficiencies and fork length bio-data are provided. Water temperature and flow data collected since the inception of the project are also presented.

Chinook, coho, steelehead, outmigrants
2006Scott River Watershed Council Fish CommitteeLimiting Factors Analysis for Coho Salmon and Other Anadromous Fish, Scott River Sub-Basin, 18010209

One of the objectives of the Scott River Watershed Council (SRWC) is to conserve and enhance the resources of the Scott River watershed. Anadromous fish are one of those resources. The SRWC wished to better direct its conservation efforts by identifying which activities and conditions in the Scott River watershed caused the greatest harm to anadromous fish. The Fish Committee of SRWC set out to accomplish this by assigning a sub-committee that would use a science-based process known as a limiting factors analysis (LFA). An LFA seeks to identify the most important environmental factors that are causing a population to decline and preventing its recovery. The information can then be used to direct efficient, effective restoration of habitat and improvement of management practices to restore anadromous species. Although the Fish Committee is concerned with steelhead, coho and Chinook salmon, the committee chose coho salmon as the focus of this LFA, because it is the most threatened. Many of the factors that limit coho salmon also limit the other anadromous species, so implementation of restoration actions for coho may help those species as well. The SRWC intends to use this LFA as a template for steelhead and Chinook LFA’s to be completed in the future. The sub-committee compiled of local citizens, landowners and agency representatives began by searching for and reviewing existing LFA’s to find an accepted protocol. It found a variety of approaches, rather than one standard protocol.

Scott River, coho, Chinook, salmon
2009McBain & Trush, Inc.Shasta River Instream Flow Methods and Implementation Framework18010209

The purpose of the project was to evaluate several alternative instream flow methods, then recommend a scientific framework and specific methods for determining instream flow needs to promote salmonid recovery and protection in the Shasta River basin. Quantifying instream flow needs is critical to restoration. Our goal was to recommend a framework best suited for the Shasta River basin that will facilitate compliance with Fish and Game Code 5937 and the Watershed-wide Permitting Program (CDFG 2008). An instream flow needs study must assess the extent to which the natural flow regime can be altered while still ensuring the health of salmonid
populations and riparian communities (Richter et al. 1997, Anderson et al. 2006). Or conversely given the status of water allocation and salmonid populations in the Shasta River basin, an instream flow needs study must determine how much additional streamfl ow is needed to promote recovery of viable salmonid populations. This determination requires a scientific framework rooted in ecological principles. An instream fl ow needs study must also be concise and transparent to ranchers, local nonprofit t groups, regulatory agency scientists and policymakers, the Resource Conservation District (RCD) staff, and other interested scientists.

Shasta, instream flow
2016Caitlin N. Jetter and William R. ChesneyShasta and Scott River Juvenile Salmonid Outmigrant Study, 2016, , 18010209

The 2016 Juvenile Salmonid Outmigrant Study is part of the ongoing work conducted annually by the California Department of Fish and Wildlife, Yreka Fisheries Program on the Shasta and Scott rivers in Siskiyou County, California. Using rotary screw traps, all age classes of outmigrating Chinook salmon (Oncorhynchus tshawytscha), coho salmon (Oncorhynchus kisutch), and steelhead trout (Oncorhynchus mykiss) were sampled from 29 January to 1 July of 2016. Mark and recapture trials were conducted multiple times per week to determine trap efficiencies and weekly population estimates. Established age-length cutoffs for each species were used to determine the age of the fish captured. In-stream conditions such as flow and water temperature were also monitored. Weekly estimates for the smolt class of all species were compared to show multi-year population trends. Using multi-year seasonal production estimates and coho salmon returns to the Shasta River, adult survival and smolt production estimates were calculated for Shasta River coho. It was estimated that for the period sampled in 2016, a total of 2,757,850 0+ Chinook, 164 1+ Chinook, 480 0+ coho, 229 1+ coho, 3 (actual number caught) 2+ coho, 11,749 0+ steelhead, 1,665 1+ steelhead, 30,501 2+ steelhead, and 6,045 3+ steelhead emigrated from the Shasta River. It was estimated for this same sample period, 56,634 0+ Chinook, 28 (actual number caught) 1+ Chinook, 14 (actual number caught) 0+ coho, 2,411 1+ coho, 1 (actual number caught) 2+ coho, 97 (actual number caught) 0+ steelhead, 73,540 1+ steelhead, and 44 (actual number caught) 2+ steelhead emigrated from the Scott River.

salmon, coho, Chinook, steelhead, Scott River, Shasta River
2009William R. Chesney, Christopher C. Adams, Whitney B. Crombie, Heather D. Langendorf, Steven A. Stenhouse and Kristen M. KirkbyShasta River Juvenile Coho Habitat & Migration Study18010209

Initial surveys of the upper Shasta River between river miles (RMs) 33.72 and 31.98 in April of 2008 determined that 0+ juvenile coho salmon (Oncorhynchus kisutch) were rearing throughout the area surveyed. Age 0+ coho salmon were captured at RM 32 and tagged with passive integrated transponder (PIT) tags in order to study migration behavior and estimate the probability of survival. A rapid increase in the maximum daily water temperatures from 21.4 degrees C in late April to over 24.2 degrees C during four consecutive days in May displaced juvenile coho from three of the four study sites between RMs 32.9 and 33.6. Some of the PIT tagged juvenile coho responded to the increase in water temperature by migrating over 4 miles upstream to areas of cold spring inflow. All observed over-summer rearing habitat utilized by coho was associated with cold springs.
Throughout the summer of 2008, coho reared successfully at three study sites on the Shasta River mainstem between RMs 36 and 36.8, where the weekly maximum temperatures ranged from 20.57 to 22.47° C. Juvenile coho were also observed rearing during the summer in Kettle Springs Creek at the outfall of Kettle Springs, in Big Springs Creek at the outfall of Big Springs Lake and at a small coldwater seep on the mainstem Shasta River at RM 33.3. Summer rearing habitat downstream of the cold spring at RM 37 on the Shasta River was impacted by water use practices including the release of warm stored water from an upstream
reservoir, diversion of spring water, and warm tailwater returning to the stream. We used a Cormack-Jolly-Seber live-recapture model (Schwarz and Seber 1999) in program MARK (White and Burnham 1999) to obtain maximum likelihood estimates of apparent survival (Φi) and recapture probability (pi) over three river segments for coho smolts emigrating from rearing habitats on the Hole in the Ground (HIG) Ranch in the spring of 2009 (3/15/09 to 5/30/09).

coho, Shasta River
2016Bruce Eddy, Chip Dale, Elizabeth Osier Moats, William TinniswoodKlamath Watershed District Stock Status Review of Native Fish, , , , , , , , , , , , 18010206

This is a technical report summarizing the status of stocks in various sub-basins of the Klamath River watershed (Oregon sub-basins only).

Oregon, bull trout, Jenny Creek sucker, Lost River sucker, Millker Lake lamprey, redband trout, Pit-Klamath brook lamprey, Shortnose sucker, Slender sculpin, Upper Klamath Lake lamprey
2005Siskiyou County Resource Conservation DistrictInitial Phase of the Scott River Watershed Council Strategic Action Plan, October 2005 Update, , , , , , 18010209

The Scott River Watershed Council (SRWC) has developed this plan for the Scott River watershed for the purpose of cooperatively establishing a common strategy for restoration and management actions. Thus, the Scott River Watershed Strategic Action Plan (SAP) will form the basis for setting priorities for future projects and practices to be supported by the SRWC, the communities within the watershed, and the many funding sources. Watershed, and Historic Watershed Conditions provides a general report which describes the planning process, history of community involvement, agency coordination, overall goals and objectives, and the background of watershed changes over time. The various sections relating to specific watershed topics (such as fisheries, water, riparian and habitat, etc.) include the following items: history; current conditions; findings; reference to
current and past actions; and the goals, objectives and strategic actions that will be used to develop projects and studies to assist in filling critical gaps. Prioritized objectives and the strategic actions are identified in the topic areas and include indicators for the term of accomplishment1 (i.e. 2 year, 5 year, 10, year and 50 year). These watershed topics will be expanded with each phase of the SAP to further define current conditions and restoration needs. Planning sections: Monitoring Plan, Developing Strategic Actions, and Outstanding Issues/Questions provide the SRWC with detailed information that will be used to develop a detailed workplan, help set priorities and identify gaps. The remaining sections: Glossary of Terms, List of Acronyms, Works Cited, and Appendices contain reference material to assist the reader with information they may not be familiar with,
provide supporting data, or for use when needing more information about a topic.

Scott River
1997Oregon Department of Fish and WildlifeKlamath River Basin, Oregon Fish Management Plan, , , , , , , , , , , 18010206

This Klamath River Basin Fish Management Plan, adopted by the Oregon Fish and Wildlife Commission on August 22, 1997, is one of many throughout Oregon that has been prepared by the Oregon Department of Fish and Wildlife (ODFW) to guide fish management within the next ten years. As the name implies, this plan addresses all of the public waters within the Klamath River Basin in Oregon, Figure 1. Streams within the basin have been put in six groupings based on their commonalties, particularly regarding the life history of redband trout. This plan also addresses 22 lakes and reservoirs within the basin. The great majority of these waters are managed by the ODFW's KlamathlLake Fish District, but the far western parts of the basin, including Howard Prairie and Hyatt reservoirs, are managed by the Upper Rogue Fish District. This plan contains four major sections: Habitat Management, Fish Management, Fish Management Direction and Alternatives, and Angler Access. In addressing these subjects, it is not intended to be an exhaustive compilation of information on these basin resources. Rather, it is intended to be an adequate overview with sufficient detail to guide decisions and future management. The Habitat Management section addresses the history of the basin and its present
status. Important habitat management considerations and limiting factors are described in general; then the habitat and the limitations of each stream and water body is briefly described. These are followed by policies and objectives for habitat management.

plan, Oregon, fish
2014NOAAFinal Recovery Plan for the Southern Oregon/ Northern California Coast Evolutionarily Significant Unit of Coho Salmon (Oncorhynchus kisutch) (SONCC), , , 180102

Thousands of coho salmon once returned to spawn in the rivers and streams of Northern California and Southern Oregon. Not long ago, these watersheds provided conditions that supported robust and resilient populations of coho salmon that could persist under dynamic environmental conditions. The combined effects of fish harvest, hatcheries, hydropower operations, and habitat alterations caused by land management led to declines in these populations. The National Marine Fisheries Service’s (NMFS) evaluation of declining coho salmon abundance and productivity, as well as range reductions and diminished life-history diversity, supported the decision to list the Southern Oregon/Northern California Coast (SONCC) Evolutionarily Significant Unit (ESU) of coho salmon as a threatened species under the Endangered Species Act (ESA) in 1997, a decision that was reaffirmed in 2005. Recovery can only be achieved through coordinated efforts to build strong conservation partnerships. Conservation partners may be individuals, groups, and government or nongovernment organizations including NMFS, industry, or tribes who have an interest in the recovery of SONCC coho salmon. The ESA envisions recovery plans as the central organizing tool for guiding each species’ recovery process. The recovery plan is a road map to recovery – it lays out where we need to go and how best to get there. The SONCC Coho Salmon ESU recovery plan (Plan) was developed to provide a roadmap to recovery of this species which conservation partners can follow together. Specifically, the Plan is designed to guide implementation of prioritized actions needed to conserve and recover the species by providing an informed, strategic, and voluntary approach to recovery that is based on the best available science. Use of a recovery plan ensures that recovery efforts target limited resources effectively and efficiently.

NOAA, SONCC, spawning habitat, coho salmon
2017U.S. Geological SurveyUpper Klamath Basin Collaborative Groundwater Monitoring, , , , , , , 180102

This web page provides access to current and historic groundwater-level data collected by monitoring partners, as well as water-level graphs and maps showing net water-level changes between any two time periods. Data for individual wells are filtered to remove measurements taken during active pumping because they do not accurately represent conditions in the aquifer.

groundwater, monitoring
2017Bureau of ReclamationBureau of Reclamation Klamath Basin Area Office, , , , , 180102

This is the website for the Klamath Project of the Bureau of Reclamation.

irrigation
2017Bureau of ReclamationBureau of Reclamation, , 180102

This website is for the Bureau of Reclamation. Established in 1902, the Bureau of Reclamation is best known for the dams, powerplants, and canals it constructed in the 17 western states. These water projects led to homesteading and promoted the economic development of the West. Reclamation has constructed more than 600 dams and reservoirs including Hoover Dam on the Colorado River and Grand Coulee on the Columbia River.

Today, we are the largest wholesaler of water in the country. We bring water to more than 31 million people, and provide one out of five Western farmers (140,000) with irrigation water for 10 million acres of farmland that produce 60% of the nation's vegetables and 25% of its fruits and nuts.

Reclamation is also the second largest producer of hydroelectric power in the United States. Our 53 powerplants annually provide more than 40 billion kilowatt hours generating nearly a billion dollars in power revenues and produce enough electricity to serve 3.5 million homes.

Picture of Hoover DamToday, Reclamation is a contemporary water management agency with a Strategic Plan outlining numerous programs, initiatives and activities that will help the Western States, Native American Tribes and others meet new water needs and balance the multitude of competing uses of water in the West. Our mission is to assist in meeting the increasing water demands of the West while protecting the environment and the public's investment in these structures. We place great emphasis on fulfilling our water delivery obligations, water conservation, water recycling and reuse, and developing partnerships with our customers, states, and Native American Tribes, and in finding ways to bring together the variety of interests to address the competing needs for our limited water resources.

Reclamation
2017U.S. Geological SurveyUSGS, , , 180102

The USGS website includes real time and historic data sets and technical reports for numerous monitoring locations throughout the Klamath Basin.

data
2017Trout UnlimitedTrout Unlimited: California and Klamath Program180102

Website links to Trout Unlimited's California and Klamath Program. Includes a listing of associated staff.

conservation
2017North Coast Regional Water Quality Control BoardNorth Coast Regional Water Quality Control Board, , , , , 18010209

This is the website for the North Coast Regional Water Quality Control Board. There are nine regional water quality control boards statewide. The nine Regional Boards are semi-autonomous and are comprised of seven part-time Board members appointed by the Governor and confirmed by the Senate. Regional boundaries are based on watersheds and water quality requirements are based on the unique differences in climate, topography, geology and hydrology for each watershed. Each Regional Board makes critical water quality decisions for its region, including setting standards, issuing waste discharge requirements, determining compliance with those requirements, and taking appropriate enforcement actions.

water quality, water rights
2017State of OregonOregon Watershed Restoration Inventory, , , , , , , , , 180102

The Oregon Watershed Restoration Inventory (OWRI) originated at the onset of the Oregon Plan for Salmon and Watersheds to track Oregonians' voluntary efforts to restore habitats for salmon and wildlife. While the database is managed by OWEB and contains information about grants funded by OWEB, the majority of the OWRI entries represent voluntary actions of private citizens and landowners who have worked in partnership with federal, state, and local groups to improve aquatic habitat and water quality conditions. OWRI is the single largest restoration information database in the Western United States with nearly 17,000 completed projects reported since 1995. This is an online reporting tool.

Oregon, habitat restoration
2015Mary Claire Kier, John Hileman, Steve CannataAnnual Report: Trinity River Basin Salmon and Steelhead Monitoring Project: Chinook and Coho Salmon and Fall-Run Steelhead Run-Size Estimates Using Mark-Recapture Methods 2014-2015 Season, , 18010209

The California Department of Fish and Wildlife's Trinity River Project conducted tagging and recapture operations from June 2014 through March 2015 to produce run-size, angler harvest, and spawner escapement estimates of spring-run (spring Chinook) and fall-run Chinook salmon [fall Chinook (Oncorhynchus tshawytscha)], coho salmon (O.kisutch), and fall steelhead (O. mykiss) in the Trinity River basin. The monitoring results
informs the Trinity River Restoration Program’s (TRRP) adaptive management decision making process and helps to evaluate progress toward achieving fundamental objectives outlined in the Integrated Assessment Plan (TRRP, 2009). Utilizing a Petersen mark-recapture methodology, we estimate a run-size of 6,959 (95% CI 6,419 – 7,523) spring Chinook migrated into the Trinity River basin upstream of Junction City weir. The run was comprised of an estimated 1,998 naturally-produced adults and 132 naturally-produced jacks and 4,300 hatchery-produced adults and 528 hatchery-produced jacks. Using tags returned by anglers we estimate 227 spring
Chinook were harvested, yielding an escapement of 6,732 fish. The escapement of 1,931 naturally-produced adult spring Chinook was 32.2% of the TRRP goal of 6,000 spring Chinook. An estimated run-size of 37,829 (95% CI 33,056 – 43,670) fall Chinook migrated past Willow Creek weir (WCW). The run was comprised of an estimated 11,017 naturally produced adults and 6,332 naturally-produced jack salmon and 19,874 hatchery produced adults and 606 hatchery-produced jacks. We estimate 926 were harvested by anglers, yielding a total escapement of 36,803 fish. The escapement of 10,700 naturally-produced adult fall Chinook was 17.4% of the 62,000 fish TRRP goal. Both the coho run-size and escapement in the Trinity above Willow Creek were estimated at 13,537 (95% CI 12,133 – 15,021), because no coho were reported as harvested.

weir, Trinity, run-size
2017California Department of Fish and WildlifeCalifornia Department of Fish and Wildlife Fisheries Branch, , , , , , , 18010209

Website links to the Fisheries Branch of the California Department of Fish and Wildlife. Website includes information on species conservation and recovery, important documents, and the Fisheries Restoration Grants Program.

salmonids, Chinook salmon, coho salmon, steelhead
2017Dr. Darren WardHumboldt State University, Department of Fisheries Biology-Dr. Darren Ward: Publications and Research, , , , 18010209

Website links to publications authored by Dr. Darren Ward, professor at Humboldt State University's Department of Fisheries Biology. Click the menu on the left to view current research, some of which is also applicable to Klamath River salmonids (although downloadable work products are not listed at this time). Dr. Ward can be reached via email at darren.ward@humboldt.edu to discuss additional questions related to his research projects.

salmonids, salmon, steelhead
2014Rebecca M. Quinones, Marcel Holyoak, Michael L. Johnson, Peter B. MoylePotential Factors Affecting Survival Differ by Run-Timing and Location: Linear Mixed-Effects Models of Pacific Salmonids (Oncorhynchus spp.) in the Klamath River, California, , , 18010209

Understanding factors influencing survival of Pacific salmonids (Oncorhynchus spp.) is essential to species conservation, because drivers of mortality can vary over multiple spatial and temporal scales. Although recent studies have evaluated the effects of climate, habitat quality, or resource management (e.g., hatchery operations) on salmonid recruitment and survival, a failure to look at multiple factors simultaneously leaves open questions about the relative importance of different factors. We analyzed the relationship between ten factors and survival (1980–2007) of four populations of salmonids with distinct life histories from two adjacent watersheds (Salmon and Scott rivers) in the Klamath River basin, California. The factors were ocean abundance, ocean harvest, hatchery releases, hatchery returns, Pacific Decadal Oscillation, North Pacific Gyre
Oscillation, El Nin˜o Southern Oscillation, snow depth, flow, and watershed disturbance. Permutation tests and linear mixedeffects models tested effects of factors on survival of each taxon. Potential factors affecting survival differed among taxa and between locations. Fall Chinook salmon O. tshawytscha survival trends appeared to be driven partially or entirely by hatchery practices. Trends in three taxa (Salmon River spring Chinook salmon, Scott River fall Chinook salmon; Salmon River summer steelhead trout O. mykiss) were also likely driven by factors subject to climatic forcing (ocean abundance, summer flow). Our findings underscore the importance of multiple factors in simultaneously driving population trends in widespread species such as anadromous salmonids. They also show that the suite of factors may differ among different taxa in the same
location as well as among populations of the same taxa in different watersheds. In the Klamath basin, hatchery practices need to be reevaluated to protect wild salmonids.

run timing, salmonids, hatchery
2014A. L. Nichols, A. D. Willis, C. A. Jeffres, and M. L. DeasWater Temperature Patterns Below Large Groundwater Springs: Management Implications For Coho Salmon In The Shasta River, California, 18010209

Elevated stream temperature is a primary factor limiting the coho salmon (Oncorhynchus kisutch) population in California’s Shasta River Basin. Understanding the mechanisms driving spatial and temporal trends in water temperature throughout the Shasta River is critical to prioritising river restoration efforts aimed at protecting this threatened species. During the summer, the majority of streamflow in the Shasta River comes from large-volume, cold-water springs at the head of the tributary Big Springs Creek. In this study, we evaluated the initial character of this spring water, as well as the downstream fate and transport of these groundwater inflows during July and August 2008. Our results indicated that Big Springs Creek paradoxically provided both cool and warm waters to the Shasta River. During this period, cool groundwater inflows heated rapidly in the downstream direction in response to thermal loads from incoming solar radiation. During the night time, groundwater inflows did not appreciably heat in transit through Big Springs Creek. These diurnally varying water temperature conditions were inherited by the Shasta River, producing longitudinal temperature patterns that were out of phase with ambient meteorological conditions up to 23 km downstream. Findings from this study suggest that large, constant temperature spring sources and spring-fed rivers impart unique stream temperature patterns on downstream river reaches that can determine reach-scale habitat suitability for cold-water fishes such as coho salmon. Recognising and quantifying the spatiotemporal patterns of water temperature downstream from large spring inflows can help identify and prioritize river restoration actions in locations where temperature patterns will allow rearing of cold-water fishes.

coho, Shasta, water temperature
2014Rebecca M. Quiñones, Theodore E. Grantham, Brett N. Harvey, Joseph D. Kiernan, Mick Klasson, Alpa P. Wintzer, Peter B. MoyleDam Removal and Anadromous Salmonid (Oncorhynchus spp.) Conservation in California, , 180102

Dam removal is often proposed for restoration of anadromous salmonid populations, which are in serious decline in California. However, the benefits of dam removal vary due to differences in affected populations and potential for environmental impacts. Here, we develop an assessment method to examine the relationship between dam removal and salmonid conservation, focusing on dams that act as complete migration barriers. Specifically, we (1) review the effects of dams on anadromous salmonids, (2) describe factors specific to dam removal in California, (3) propose a method to evaluate dam removal effects on salmonids, (4) apply this method to evaluate 24 dams, and (5) discuss potential effects of removing four dams on the Klamath River. Our flexible rating system can rapidly assess the likely effects of dam removal, as a first step in the prioritization of multiple dam removals. We rated eight dams proposed for removal and compared them with another 16 dams, which are not candidates for removal. Twelve of the 24 dams evaluated had scores that indicated at least a moderate benefit to salmonids following removal. In particular, scores indicated that removal of the four dams on the Klamath River is warranted for salmonid conservation. Ultimately, all dams will be abandoned, removed, or rebuilt even if the timespan is hundreds of years. Thus, periodic evaluation of the environmental benefits of dam removal is needed using criteria such as those presented in this paper.

dam removal
2013Thomas H. Williams, John Carlos Garza, Nicholas J. Hetrick, Steven T. Lindley, Michael S. Mohr, James M. Myers, Michael R. O’Farrell, Rebecca M. Quiñones, David J. TeelUpper Klamath and Trinity River Chinook Salmon Biological Review Team Report, 180102

In response to a petition to list under the U.S. Endangered Species Act both spring-run and fall-run Chinook salmon in the Upper Klamath and Trinity Rivers (UKTR) Chinook Salmon Evolutionarily Significant Unit (ESU) the National Marine Fisheries Service (NMFS) Southwest Fisheries Science Center convened a Biological Review Team (BRT) to evaluate new information they determined to be most relevant to the questions of ESU
configuration and status. This included information provided by the Petitioners in their petition, information deemed pertinent by the BRT, and information provided to the NMFS Southwest Regional Office by other parties interested in this issue. The purpose of this Technical Memorandum is to document the BRT’s review and analysis of this information and to report their findings. Most importantly, the BRT concluded that the new information supported the existing UKTR Chinook ESU configuration with springrun and fall-run populations included in a single ESU, and that the ESU is currently at a low risk of extinction within the next 100 years.

Chinook salmon
2011Jack Stanford, Walter Duffy, Eli Asarian, Brian Cluer, Phil Detrich, Lorri Eberle, Steve Edmondson, Scott Foott, Mark Hampton, Jacob Kann, Kevin Malone, Peter MoyleConceptual Model for Restoration of the Klamath River – Chapter 7, , , , 180102

The goal of this paper is to provide a conceptual model to underpin plans for restoration of salmon, resident fishes and other key attributes of the Klamath River Ecosystem. We include boundaries, principles, and assumptions for the Klamath River Ecosystem, with a scientific retrospective analysis serving as the basis for our conceptual model. The authors represent a broad range of professional expertise with many years of
research and management experience in the Klamath and other western USA rivers.We start with our view of what a conceptual model should be and then move to descriptions of Klamath Basin physiography and geopolitics. Then we present a retrospective analysis of Klamath biogeography and human influences on aquatic species in relation to functional domains of the river system. The paper concludes with our conceptual model for the Klamath River Ecosystem as derived from our collective understanding of natural and cultural attributes, interactions, constraints and opportunities.

restoration
2013Rebecca M. Quiñones, Michael L. Johnson, Peter B. MoyleHatchery Practices May Result in Replacement of Wild Salmonids: Adult Trends in the Klamath Basin, California, , , 18010209

Appraisal of hatchery-related effects on Pacific salmonids (Oncorhynchus spp.) is a necessary component of species conservation. For example, hatchery supplementation can influence species viability by
changing genetic, phenotypic and life-history diversity. We analyzed time series data for seven salmonid taxa from the Klamath River basin, California, to investigate trajectories of wild and hatchery adult populations.
Linear regression coupled with randomized permutations (n=99,999), two- tailed t tests, and Bayesian change point analysis were used to detect trends over time. Cross correlation was also used to evaluate relationships
between wild and hatchery populations. The taxa of interest were spring, fall, and late-fall Chinook Salmon (O. tshawytscha); Coho Salmon (O. kisutch); Coastal Cutthroat Trout (O. clarki clarki); and summer
and hybrid Steelhead Trout (O. mykiss). Significant decreases were detected for summer and hybrid Steelhead Trout. The proportion of wild fall Chinook has also significantly decreased concurrently with increases in hatchery returns. In comparison, returns of most Chinook and coho runs to the hatcheries, and fall Chinook strays to wild spawning areas from Iron Gate Hatchery have significantly increased since the 1970s.
Increases were also detected for wild late-fall Chinook and spring Chinook adults. However, both of these were significantly correlated with Chinook Salmon returns to Trinity River Hatchery, suggesting augmentation by
hatchery strays. Changes in abundances appeared related to changing ocean habitat conditions and hatchery practices. Our results suggest that anadromous salmonid populations in the Klamath River basin are becoming
increasingly dependent on hatchery propagation, a pattern that can threaten population persistence.

hatcheries, hatchery, salmon, steelhead
2016Brian W. Hodge, Margaret A. Wilzbach, Walter G. Duffy, Rebecca M. Quiñones & James A. HobbsLife History Diversity in Klamath River Steelhead, 18010209

Oncorhynchus mykiss exhibits a vast array of life histories, which increases its likelihood of persistence by spreading riskof extirpation among different pathways. The Klamath River basin (California–Oregon) provides a particularly interesting backdrop for the study of life history diversity in O. mykiss, in part because the river is slated for a historic and potentially influential dam removal and habitat recolonization project. We used scale and otolith strontium isotope (87Sr/86Sr) analyses to characterize life history diversity in wild O. mykiss from the lower Klamath River basin. We also determined maternal origin (anadromous or nonanadromous) and migratory history (anadromous or nonanadromous) of O. mykiss and compared length and fecundity at age between anadromous (steelhead) and nonanadromous (Rainbow Trout) phenotypes of O. mykiss. We identified a total of 38 life history categories at maturity, which differed in duration of freshwater and ocean rearing, age at maturation, and incidence of repeat spawning. Approximately 10% of adult fish sampled were nonanadromous. Rainbow Trout generally grew faster in freshwater than juvenile steelhead; however, ocean growth afforded adult steelhead greater length and fecundity than adult Rainbow Trout. Although 75% of
individuals followed the migratory path of their mother, steelhead produced nonanadromous progeny and Rainbow Trout produced anadromous progeny. Overall, we observed a highly diverse array of life histories among Klamath River O. mykiss. While this diversity should increase population resilience, recent declines in the abundance of Klamath River steelhead suggest that life history diversity alone is not sufficient to stabilize a population.

Steelhead
2017Various agencies and tribesCDEC Shasta River Basin Data, , 180102

CDEC website links to all monitoring stations on within the Shasta River basin for water quality, water temperature, and instream flows. Click on hyperlink of station code in first column to access available data sets. Data has been provided by various state agencies, federal agencies, tribes, and the Shasta Valley Resource Conservation District.

water quality data, instream flow data, data
2017Various agencies and tribesCDEC Scott River Basin Data, , 180102

CDEC website includes all Scott River basin monitoring stations for water quality and instream flows. To access a monitoring station, click the hyperlink the first column. Data has been contributed by various state agencies, federal agencies, and tribes.

water quality data, instream flow data
2017California Department of Water Resources, U. S. Fish & Wildlife Service, Yurok Tribe, Karuk Tribe, U.S. Bureau of Reclamation, U.S. Geological SurveyCDEC Klamath River Basin Data, , 180102

CDEC website links to all mainstem Klamath related water quality and flow monitoring data from Clear Lake and the A Canal downstream to the mouth of the Klamath. Data is from multiple sources. To access data, click on the hyperlinked Station ID in the first column to see available datasets and time periods. Note USGS data is redundant with what is posted on the USGS website for identical stations (e.g., Klamath River at Iron Gate).

water quality data, flow data
2012Deborah L. HathawayStream Depletion Impacts Associated with Pumping from Within or Beyond the “Interconnected Groundwater” Area as Defined in the 1980 Scott Valley Adjudication, 18010209

This memorandum describes an analysis of stream depletion impacts associated with pumping from two areas within the Scott Valley. One area is that within the zone of “Interconnected Groundwater” as delineated in the 1980 Scott Valley Adjudication. The second area is the area of alluvial fill within the Scott Valley that falls outside of the boundaries of the above-referenced zone. The analysis uses the Scott Valley Groundwater Model prepared by S.S. Papadopulos & Associates, Inc. (July 2012).

groundwater, Scott River
2012S.S. Papadoplos & Associates, Inc. Groundwater Conditions in Scott Valley, California, , 18010209

This report describes groundwater conditions in the Scott Valley, located in Siskiyou County, California, and the development of a groundwater model representing the alluvial aquifer that can be used to investigate roundwater/surface-water interactions. The goal of this work is to improve understanding of the relationship between land and water use on flow conditions in the Scott River. The groundwater model is applied to examine groundwater conditions given recent levels of groundwater use, and under an alternative water use condition representing partial build-out of the existing groundwater capacity. The partial build-out case, in comparison to the recent condition case, provides a mechanism for examining the impacts of groundwater pumping on the aquifer and on the Scott River. Many other scenarios can be evaluated through specification of alternative conditions to the model input packages. For example, scenarios may be structured to examine how the location and timing of groundwater diversion and use, or how managed recharge, might enhance late season flows
of the Scott River.

groundwater, Scott River
2017California Department of Fish & WildlifeScott River and Shasta River Instream Flow Study Plan Development, , , , , 18010209

Scott River and Shasta River Instream Flow Study Plan Development. This site provides project materials for instream flow studies for the Shasta and Scott Rivers.

Study Plans, LIAM Process, Fish Passage, Mesohabitat Delineation
2016Russell W. Perry, John M. Plumb, Edward Jones, Nicholas A. Som, Nicholas J. Hetrick, Thomas B. HardyAn Overview of the Stream Salmonid Simulator for the Trinity River, , , , , 18010209

An Overview of the Stream Salmonid Simulator for the Trinity River. This presentation provides information on the Relevance to Decision Support System, Underlying Basis and Structure, Running S3 for DSS Workshop and Model output for 2012 for the Trinity River.

Decision Support System, fish habitat
2016Russell W. Perry, John M. Plumb, Nicholas A. Som, Nicholas Hetrick, Thomas HardyModeling Fish Movement in a Spatially Explicit Population Model of Juvenile Chinook Salmon in the Klamath River, USA180102

Movement of individuals through space is a common feature of life cycle models that simulate the effects of spatial variation in the environment on population dynamics. Movement models range in biological realism from simple meta-population models that keep track of the number of individuals in each sub-population to complex individual based approaches that keep track of the xy-coordinates of each individual in continuous space. We present an approach that is intermediate between these two extremes. We simulated movement of juvenile Chinook salmon by casting a continuous advection-diffusion model in terms of a discrete habitat template that represents the river as a mosaic of meso-habitat units. Movement is achieved by assigning the probability that fish in habitat unit h move to unit i in one time step. These movement probabilities are determined by integrating the advection-diffusion model between habitat unit boundaries. This approach has a number of advantages. First, movement is determined by two biologically meaningful parameters: the rate of migration and the rate of population spreading. Second, this movement model naturally accounts for variation in the model’s spatial (e.g., length of each habitat unit) or temporal (e.g., daily or weekly) resolution. Last, many different models of movement can be constructed from this general framework by allowing r and to vary with environmental or individual covariates. We illustrate application of this model to juvenile Chinook salmon in the Klamath River, USA, where movement rate varies as a function of fish density and size in each habitat unit.

modeling
2013Lorne A. Greig, David R. Marmorek, Carol Murray, Donald C. E. RobinsonInsight into Enabling Adaptive Management

The U.S. National Commission on Science for Sustainable Forestry recognized a need for effective adaptive management to support management for biological diversity. However, difficulties in implementing adaptive management in the U.S. Northwest Forest Plan led the Commission to wonder if comparisons across multiple adaptive management trials in the forest sector could provide insight into the factors that serve to enable or inhibit adaptive management. This comparison and the resulting discussions among a group of seasoned practitioners, with adaptive management experience at a variety of scales and levels of complexity, led to insights into a hierarchy of ten factors that can serve to either enable or inhibit implementation. Doing high quality adaptive management is about doing good science to enable learning from management experience. Enabling adaptive management though is about working with people to understand their concerns, to develop a common understanding and an environment of trust that allows adaptive

Adaptive Management cycle, Community Involvement, Planning
2017Karuk TribeKaruk Tribe-Natural Resources Department, , , 18010209

The Mission of the Karuk Department of Natural Resources is to protect, enhance and restore the cultural/natural resources and ecological processes upon which Karuk people depend. Natural Resources staff ensure that the integrity of natural ecosystem processes and traditional values are incorporated into resource management strategies.

karuk, tribes
2015David Marmorek, Carol Murray, Marc NelitzAdaptive Management and the Missouri River Recovery Program: Attributes of Effective Governance for AM

This discussion paper presents a summary of first principles and key attributes related to effective governance in the context of Adaptive Management (AM). It draws upon lessons learned from other AM programs, primarily in North America. The intent is to organize this experience to provide insight and stimulate discussion for those working on the collaborative development of an effective system of governance for AM in the Missouri River Recover Program (MRRP). This document is not meant to be prescriptive about what type of governance should be established.

Although several definitions of governance are available, a broadly held view is that it includes a consideration of authority, decision-making, and accountability. The concept of “adaptive governance” has recently emerged in the context of AM which adds a consideration of the need for organizational and institutional flexibility to cope with uncertainty and change.

While AM has been applied for several decades, implementation has not been easy. Obstacles include concerns that implementing and rigorously evaluating management actions different from the status quo may be too costly, too risky, and/or contrary to values of some stakeholders, as well as perceptions that a shift to AM threatens existing management, research and monitoring programs. Effective governance can help to address some of these obstacles by openly addressing differences in value preferences and beliefs about causation, which tend to be at the root of disagreements that inhibit progress on AM.

Governance
2017U.S. Fish and Wildife ServiceKlamath Basin National Wildlife Refuge Complex, , 18010206

Website links to all of the refuges in the Upper Klamath Basin, including Tule Lake, Lower Klamath, Clear Lake, and Bear Valley.

refuges, wildlife refuges
2017Six Rivers National Forest, USDASix Rivers National Forest, , , 18010209

This is the website for the Six Rivers National Forest, which is the primary national forest along the lower and mid Klamath River and tributaries, including the Trinity. The Six Rivers National Forest lies east of Redwood State and National Parks in northwestern California. It is a long, narrow piece of land that stretches about 140 miles from the Oregon border south to Mendocino County. It encompasses 957,590 National Forest acres and 133,410 acres of other ownership. Smith River National Recreation Area and Orleans, Lower Trinity, and Mad River Ranger Districts make up the Forest. The Forest lies in Del Norte County (43%), Humboldt County (35%), Trinity County (21%), and Siskiyou County (1%).

forest, upland, sediment, land management
2004Andrea J. Atkinson, Peter C. Trenham, Robert N. Fisher, Stacie A. Hathaway, Brenda S. Johnson, Steven G. Torres, Yvonne C. MooreDesigning Monitoring Programs in an Adaptive Management Context for Regional Multiple Species Conservation Plans,

Increasing numbers of regional, multiple species conservation plans have been developed in California since the early 1990s. However, building effective monitoring and adaptive management programs to support these plans has remained a challenge. In addition to collecting data on the status of resources and the results of management actions, monitoring programs for these plans need to resolve critical uncertainties and channel information into effective decision making. Because of the broad goals of many regional conservation plans, monitoring programs need to address ecosystem integrity and biodiversity while also tracking species “covered” by plan permits.

In this document we provide a step-by-step procedure for developing effective monitoring programs in an adaptive management context. The guidance provided here has been gleaned from experience with large multiple species plans in southern California. The process begins with clearly defining program objectives, partitioning the program into manageable but meaningful pieces, and developing management-oriented conceptual models of system function. Then, based on the objectives and conceptual models, monitoring recommendations and critical uncertainties can be identified and a coordinated program designed. We include practical examples and insights from programs in southern California and discuss the evolution of monitoring and adaptive management programs through three successive stages: 1) inventorying resources and identifying relationships; 2) pilot testing of long-term monitoring and resolving critical management uncertainties; and 3) implementing long-term monitoring and adaptive management. Ultimately, the success of regional conservation planning depends on the ability of monitoring programs to confront the challenges of adaptively managing and monitoring complex ecosystems and diverse arrays of sensitive species.

conservation, ecosystem integrity, critical uncertainties, decision-making
2009N. J. Hetrick, T. A. Shaw, P. Zedonis, J. C. Polos, and C. D. ChamberlainCompilation of Information to Inform USFWS Principals on the Potential Effects of the Proposed Klamath Basin Restoration Agreement (Draft 11) on Fish and Fish Habitat Conditions in the Klamath Basin, with Emphasis on Fall Chinook Salmon, 180102

This document is a compilation and summary of various modeling exercises, analyses, and relevant information relating to the potential effects of implementing the proposed Klamath Basin Restoration Agreement (KBRA- Draft 11) on fish and fish habitats during the interim years prior to and following the removal of PacifiCorp Hydropower Project dams (J C. Boyle, Copco 1 and 2, and Iron Gate) from the mainstem Klamath River, as proposed in the Draft Klamath Hydroelectric Settlement Agreement (KHSA). This report focuses primarily on the effects of the proposed Agreements on anadromous species, with emphasis on fall run Chinook salmon due to the relative abundance of existing data and modeling tools developed for this stock. This report does not assess interim measures specified in the Draft KHSA, and is not a comprehensive assessment of the potential effects of the KBRA’s water allocation plan, or the proposed removal of the PacifiCorp dam complex specified in the Draft KHSA. We anticipate that if the Agreements are implemented, more detailed evaluations will be conducted through a Secretarial Determination and NEPA process.In this report, we evaluate one possible hydrologic modeling scenario of KBRA implementation (WRIMS Run-32 Refuge), and compare the results to alternative flow schedules based on our current understanding of fish habitat needs, derived from flow habitat relationships described previously in the Hardy et al. (2006) “Phase II” instream flow report. More recent WRIMS model runs prepared by settlement parties are not included here, as they were completed after our analyses were finalized. We also evaluated results of a fall Chinook production model (SIAM), water quality models, and reviewed literature to describe the probable effects of the KBRA water allocation plan and restoration actions on water quantity, water quality, geomorphology, and fish health.

2010John Hefner, PBS&JExpert Review of Hetrick et. al 2009: Compilation of Information to Inform USFWS Principals on the Potential Effects of the Proposed Klamath Basin Restoration Agreement (Draft 11) on Fish and Fish Habitat Conditions in the Klamath Basin, with Emphasis on Fall Chinook Salmon, 180102

This memorandum presents a summary of the major comments submitted to PBS&J by two independent expert reviewers of Hetrick, N.J., et. al. (2009). Compilation of information to inform USFWS principals on the potential effects of the proposed Klamath Basin Restoration Agreement (Draft 11) on fish and fish habitat conditions in the Klamath Basin, with emphasis on fall Chinook salmon. Arcata Fisheries Technical Report TR 2009-11. U.S. Fish
and Wildlife Service. The complete comments of the reviewers follow the summary.

fish habitat, salmon, fall Chinook
2010J. L. Bartholomew, J. S. FoottCompilation of Information Relating to Myxozoan Disease Effects to Inform the Klamath Basin Restoration Agreement180102

This technical report describes how myxozoan disease effects on juvenile Chinook and coho salmon are predicted to differ between the scenarios of current conditions and removal of the four Klamath project dams. We begin by summarizing what we know about the effects of myxozoan pathogens on Chinook salmon, the parasite life cycles, their distribution in the Klamath River and characteristics of the polychaete host that may be
affected by changes in river management. We then look at how the two proposed scenarios will affect each of these parameters, supporting our predictions with available data. It must be taken into account that parasite infectious dose is the primary metric that will influence disease severity. This assessment is structured to prioritize the factors we believe are most important for predicting where disease effects will occur under current conditions and where future areas of high infections might occur.

fish disease, KBRA
2011Ron ColeEffects of the Klamath Basin Restoration Agreement to Lower Klamath, Tule Lake and Upper Klamath National Wildlife Refuge, , 18010206

Provisions within the KBRA, particularly those related to water, potentially effect refuge biological resources. This document seeks to explore effects to these refugees under current Project operations, (termed No Action) compared to management under provisions of the KBRA. The analysis will focus on effects to water availability, wetland habitats, and migratory birds with an emphasis on wetland dependent species.

wetland, refuges
2017California Hatchery Review ProjectCalifornia Hatchery Review Project-Klamath/Trinity, 18010209

The Iron Gate Hatchery Review assessed the Coho, Fall Chinook, and Steelhead program. An appropriation for California hatchery review was provided to the US Fish and Wildlife Service and was administered through the Pacific States Marine Fisheries Commission. The review examined hatchery programs in the Klamath, Trinity and Central Valley basins. The goal of this hatchery program review initiative is to ensure that anadromous hatchery programs in California are managed and operated to meet one or both of the primary purposes for hatcheries: (1) Helping recover and conserve naturally spawning salmon and steelhead populations, and (2)
Supporting sustainable fisheries with little or no deleterious consequence to natural populations. Eleven fishery scientists and biologists were appointed to the California Hatchery Scientific Review Group (California HSRG). Members affiliated with agencies did not represent their respective organizations. Instead they were expected to bring their individual scientific expertise to the table. The intent of this approach was to ensure that the California HSRG maintained independence and impartiality, while at the same time assuring that it possessed thorough knowledge of salmonid populations and hatchery programs in the Klamath / Trinity and Central Valley regions. The California HSRG was assisted in their deliberations by consultants affiliated with D.J. Warren & Associates, Inc. including Malone Environmental Consulting, Meridian Environmental, Inc. and ICF International. The primary role of the consultants was to assemble and organize existing data concerning operation and performance of the majority of California’s salmon and steelhead hatcheries and to identify current scientific literature that seemed most pertinent to operation and management of these hatcheries.

hatchery, hatcheries, Iron Gate
2009Alec G. Maule, Scott P. VanderKooi, John Hamilton, Richard Stocking, and Jerri BartholomewPhysiological Development and Vulnerability to Ceratomyxa Shasta of Fall-run Chinook Salmon in the Upper Klamath River Watershed18010206

We evaluated a stock for restoring runs of fall Chinook salmon Oncorhynchus tshawytscha in the Upper Klamath River basin by monitoring its development in Iron Gate Hatchery and in net-pens in the Williamson River and Upper Klamath Lake in Oregon. We transferred age-1 hatchery fall Chinook salmon to net-pens in October 2005 and age-0 fall Chinook salmon in May 2006. Indices of smolt development were assessed in the hatchery and after 3 and 14 d in net-pens. Based on gill Na+, K+-ATPase activity and plasma thyroxine (T4) concentration, age-1 Chinook salmon were not developing smolt characteristics in the hatchery during October. Fish transferred to the river or lake had increased plasma cortisol in response to stress and increased T4 accompanying the change in water, but they did not have altered development. Variables in the age-0 Chinook salmon indicated that the fish in the hatchery were smolting. The fish in the river net-pens lost mass and had gill ATPase activity similar to that of the fish in the hatchery, whereas the fish transferred to the lake gained mass and length, had reduced condition factor, and had higher gill ATPase than the fish in the river. These results, along with environmental variables, suggest that the conditions in the lake were more conducive to smoltification than those in the river and thus accelerated the development of Chinook salmon. No Chinook salmon in the hatchery or either net-pen became infected with the myxosporean parasite Ceratomyxa shasta (the presence of which in the river and lake was confirmed) during either trial or when held for 90 d after a 10-d exposure in net-pens (2006 group). We concluded that that there is little evidence of physiological impairment or significant upriver vulnerability to C. shasta among this stock of fall Chinook salmon that would preclude them from being reintroduced into the Upper Klamath River basin.

C. shata, fish disease, Chinook, Upper Klamath
2017Siskiyou CountySiskiyou County Website18010209

Website for Siskiyou County, California.

Siskiyou County, local government
2017State of CaliforniaCalifornia Fish and Game Code, , , , , , , , 18010209

This website links to the State of California's Fish and Game code, which includes all laws and regulations pertaining to salmonids and other non-anadromous species in California waters. Division 6 (Fish) includes information on the Trinity and Klamath River Fish and Game District (Chapter 2, Article 3), Dams and Obstructions (Chapter 3, Article 2), and the Salmon, Steelhead Trout, and Anadromous Fisheries Program Act and Program (Chapter 8). Use the "Text Search" feature to search for key words such as "habitat restoration," or "Klamath."

rules, regulations
2016State of OregonOregon Fish Policy and Rules, , , , , , , , , , , 18010206

Website contains State of Oregon's rules for Fish Management Plans and policies. Pertinent sections include 635-500-3640 (Klamath River from the state line to Upper Klamath Lake) and 635-500-3890 (Chinook Salmon in Upper Klamath Lake and Tributaries/reintroduction plan). Policies also pertain to Redband trout and other non-anadromous species in the Klamath Basin. Use the search feature in web browser to target policy number, water body, key words, or species name.

rules, regulations
2017Yurok Tribal Fisheries DepartmentYurok Tribal Fisheries Department Document Library, 18010209

This link leads to the document library curated by the Yurok Tribe Fisheries Department, including numerous technical reports assessing the mainstem lower Klamath River and estuary, Trinity River, and tributaries to the lower Klamath River. Reports assess fish health, run size, large wood, habitat restoration, riparian restoration, juvenile fish studies, adult fish studies, lamprey studies, and many more. Reports from 1998 through present day are included.

salmon, habitat restoration, tribes, fish health, lamprey, Chinook, coho, steelhead
2017Mid Klamath Watershed CouncilMid Klamath Watershed Council Document Library, , 18010209

This is a document library curated by the Mid Klamath Watershed Council containing links to reports related to the Klamath River, cultural ecohistory, salmon, salmon restoration, and water quality Available reports include:

•CDFG September 2002 Klamath River Fish Kill: Final Analysis of Contributing Factors and Impacts
•The Effect of the Klamath Hydroelectric Project on Traditional Resource Uses and Cultural Patterns of the Karuk People Within the Klamath River Corridor
•Toxic Algae Plagues Klamath Reservoirs
•Copco/Irongate Reservoir Toxic Cyanobacteria Results: Follow-up
•Combat_Biology_on_the_Klamath.pdf
•‘Combat Biology’ on the Klamath
•Turbulence in the Klamath River Basin
•CDFG California Salmonid Stream Habitat Restoration Manual
•2008 DFG Klamath Tributary Fish Passage Improvement Results
•Restoring Coho Salmon in the Klamath River - One Beaver At A Time

salmon, habitat restoration, water quality
2016Pacific Fishery Management Council Klamath River Technical TeamOcean Abundance Projections and Prospective Harvest Levels Klamath River Fall Chinook, 2016 Season, 18010209

This report describes the data and methods used by the Klamath River Technical Team (KRTT) to estimate age-specific numbers of fall Chinook salmon returning to the Basin in 2016. The estimates provided in this report are consistent with the Klamath Basin Megatable (CDFW) and with the 2016 forecast of ocean stock abundance. Age-specific escapement estimates for 2016 and previous years, coupled with the coded-wire tag (CWT) recovery data from Basin hatchery stocks, allow for a cohort reconstruction of the hatchery and natural components of Klamath River fall Chinook salmon (Goldwasser et al. 2001, Mohr 2006a, KRTT 2016). Cohort reconstruction enables forecasts to be developed for the current year’s ocean stock abundance, ocean fishery contact rates, and percent of spawners expected in natural areas (KRTT 2016). These forecasts are necessary inputs to the Klamath Ocean Harvest Model (Mohr 2006b), the model used by the Pacific Fishery Management Council to forecast the effect of fisheries on Klamath River fall Chinook salmon.

Chinook, harvest, run size
2009Trinity River Restoration Program and ESSA Technologies Ltd.Integrated Assessment Plan Version 1.0, , 18010209--

The Trinity River Flow Evaluation (TRFE, USFWS and HVT, 1999) recommended a restoration strategy for the Trinity River that integrates restoration of riverine processes with the instream flow-dependent needs of salmonids. This strategy is intended to rehabilitate the river ecosystem to improve and maintain the fish and wildlife resources of the Trinity River through managed flows combined with mechanical rehabilitation and coarse sediment augmentation projects. The subsequent EIS/EIR and Record of Decision (ROD, DOI 2000) selected the TRFE recommendations, plus a watershed restoration component, as the Preferred Alternative for restoring the mainstem fishery resources and native wildlife of the Trinity River. The TRFE and ROD provide a restoration strategy for the Trinity River Restoration Program (hereafter called the Program) but did not specify methods for assessing the effectiveness of the TRFE and ROD management actions in achieving Program goals or management targets. To fill this need, the Integrated Assessment Plan (IAP) identifies key assessments that:
1. evaluate long-term progress toward achieving Program goals and objectives; and 2. provide short-term feedback to improve Program management actions by testing key hypotheses and reducing management uncertainties.

Trinity, adaptive management
2012U.S. Fish and Wildlife ServiceRevised Recovery Plan for the Lost River Sucker and Shortnose Sucker, , 18010203

The goal of our recovery program is to arrest the decline and enhance Lost River sucker and shortnose sucker populations so that Endangered Species Act protection is no longer necessary. Demographic-based and threats-based objectives will facilitate recovery and enable attainment of the recovery goal. Demographic-based objectives include increasing larval production, individual survival and recruitment to Revised Lost River Sucker and Shortnose Sucker Recovery Plan spawning populations, and therefore abundance in spawning populations. The objectives of restoring spawning and nursery habitat, expanding reproduction, reducing the negative impacts from water quality on all life stages, clarifying the effects of other species on all life stages, reducing entrainment, and establishing auxiliary populations comprise the threats-based objectives. The recovery strategy is intended to produce and document healthy, self-sustaining populations by reduction of mortality, restoration of habitat, including spawning, larval and juvenile habitats, and increasing connectivity between spawning and rearing habitats. It also involves ameliorating adverse effects of degraded water quality, disease, and non-native fish. The plan provides areas of emphasis and guidelines to direct recovery actions. Recent, 5-year status reviews for each species assigned a recovery priority number of 4C for both species (USFWS 2007a, b). However, shortnose sucker were inaccurately assigned given that they do not belong to a monotypic genus.

suckers
2014R.J. Peters, J.J. Duda, G.R. Pess, M. Zimmerman, P. Crain, Z. Hughes, A. Wilson, M.C. Liermann, S.A. Morley, J. McMillan, K. Denton, and K. WarheitGuidelines for Monitoring and Adaptively Managing Restoration of Chinook Salmon and Steelhead on the Elwha River, ,

As of January, 2014, the removal of the Elwha and Glines Canyon dams on the Elwha River, Washington, represents the largest dam decommissioning to date in the United States. Dam removal is the single largest step in meeting the goals of the Elwha River Ecosystem and Fisheries Restoration Act of 1992 (The Elwha Act) — full restoration of the Elwha River ecosystem and its native anadromous fisheries (Section 3(a)). However, there is uncertainty about project outcomes with regards to salmon populations, as well as what the ‘best’ management strategy is to fully restore each salmon stock. This uncertainty is due to the magnitude of the action, the large volumes of sediment expected to be released during dam removal, and the duration of the sediment impact period following dam removal. Our task is further complicated by the depleted state of the native salmonid populations remaining in the Elwha, including four federally listed species. This situation lends itself to a monitoring and adaptive management approach to resource management, which allows for flexibility in decision-making processes in the face of uncertain outcomes.

The Elwha Monitoring and Adaptive Management (EMAM) guidelines presented in this document provide a framework for developing goals that define project success and for monitoring project implementation and responses, focused upon two federally listed salmon species — Puget Sound Chinook salmon (Oncorhynchus tshawytscha) and Puget Sound steelhead (O. mykiss). The framework also should serve as a guide to help managers adaptively manage fish restoration actions during and following dam removal.

dam removal, monitoring
2016M. Brady Allen, Rod O. Engle, Joseph S. Zendt, Frank C. Shrier, Jeremy T. Wilson, Patrick J. ConnollySalmon and Steelhead in the White Salmon River After the Removal of Condit Dam–Planning Efforts and Recolonization of Results,

Condit Dam, at river kilometer 5.3 on the White Salmon River, Washington, was breached in 2011 and completely removed in 2012. This action opened habitat to migratory fish for the first time in 100 years. The White Salmon Working Group was formed to create plans for fish salvage in preparation for fish recolonization and to prescribe the actions necessary to restore anadromous salmonid populations in the White Salmon River after Condit Dam removal. Studies conducted by work group members and others served to inform management decisions. Management options for individual species were considered, including natural recolonization, introduction of a neighboring stock, hatchery supplementation, and monitoring natural recolonization for some time period to assess the need for hatchery supplementation. Monitoring to date indicates that multiple species and stocks of anadromous salmonids are finding and spawning in the now accessible and recovering habitat.

dam removal, salmon
2017National Park ServiceElwha Fish Restoration, Olympic National Park,

Website includes final fish restoration plans for various species, Final EIS, and other technical documents related to the removal of the dams on the Elwha River.

Elwha, dam removal
2017U.S. Fish and Wildlife ServiceU. S. Fish and Wildlife Service (Arcata) Listing of Technical Reports and Data Sets for the Klamath and Trinity, , , , 18010209--

This website includes numerous technical reports and datasets finalized by the U.S. Fish and Wildlife Service Arcata Field Office. Reports include juvenile salmonid monitoring, redd surveys, habitat assessments, water temperature monitoring and modeling, emirgration monitoring, and disease studies, among numerous others, Tehcnical reports focus on the Lower Klamath, Mid-Klamath, Scott, Shasta, and Trinity watersheds.

salmon, steelhead, lamprey
2011Peter B. Adams, L.B, Boydstun, Sean P. Gallagher, Michael K. Lacy, Trent McDonald, and Kevin E. ShafferCDFW Fish Bulletin 180:, , , , 18010209

California’s salmon and steelhead populations have experienced marked declines leading to listing of almost all of California’s anadromous salmonids under the California Endangered Species Act (CESA) and Federal Endangered Species Act (ESA). Both CESA and ESA listings require recovery plans that call for monitoring to provide some measure of progress toward recovery. In addition, there are related monitoring needs for other management activities such as hatchery operations and fisheries management. This California Coastal Salmonid Monitoring Plan (CMP) has been developed to meet these monitoring needs, describing the overall strategy, design, and methods used in monitoring salmonid populations. Implementation details of the plan are described in Shaffer (in prep.). The CMP uses the Viable Salmonid Population (VSP; McElhany et. al. 2000) concept as the framework for plan development. The VSP conceptual framework assesses salmonid viability in terms of four key population characteristics: abundance, productivity, spatial structure, and diversity. High abundance buffers a population against both ‘normal’ and catastrophic variation due to environmental conditions and loss due to anthropogenic factors. High productivity will lead to more certain replacement when populations are placed under either natural or anthropogenic stress. Wide spatial structure reduces extinction risk due to catastrophic events and provides pathways for recolonization. Diversity in life history traits (e.g., time of spawning, juvenile life history, adult fish size, age structure, degree of anadromy, etc.) provides resilience against extinction risk from changing conditions.

coho, monitoring
2017California Department of Fish and WildlifeCalifornia Department of Fish and Wildlife Listing of Klamath/Trinity Biological Information Documents, , 18010209--

This website contains a listing of documents pertinent to the Klamath/Trinity Program, including historical documents, Trinity River Project and Klamath River Project annual reports, semi real time weir counts, semi real time hatchery returns, semi real time harvest estimates and reference materials related to the fisheries and restoration of the Klamath and Trinity Basins.

coho, Chinook, hatchery, habitat restoration, annual reports
2014California Department of Fish and Wildlife, Mary Claire Kier, John Hileman, and Steve CannataAnnual Report: Trinity River Basin Salmon and Steelhead Monitoring Project: Chinook and Coho Salmon and Fall-Run Steelhead Run-Size Estimates Using Mark-Recapture Methods, 2013-2014 Season18010209

The California Department of Fish and Wildlife's Trinity River Project conducted tagging and recapture operations from June 2013 through March 2014 to produce run-size, angler harvest, and spawner escapement estimates of spring-run (spring Chinook) and fall-run Chinook salmon [fall Chinook (Oncorhynchus tshawytscha)], coho salmon (O. kisutch), and fall steelhead (O. mykiss) in the Trinity River basin. This information is produced for the Trinity River Restoration Program (TRRP) to help evaluate progress toward program objectives outlined in the Integrated Assessment Plan (TRRP, 2009) Utilizing a Petersen mark-recapture methodology, we estimate a run-size of 8,961 spring Chinook migrated into the Trinity River basin upstream of Junction City weir. Using tags returned by anglers we estimate 254 spring Chinook were harvested, yielding an escapement of 8,707 fish. The 2013 run of spring Chinook was comprised of an estimated 2,669 naturally-produced adults and 146 jacks and 6,011 hatchery-produced adults and 135 hatchery-produced jacks. The post-harvest escapement of 2,591 naturally-produced adult spring Chinook was 43.2% of the TRRP goal of 6,000 spring Chinook. An estimated run-size of 36,989 fall Chinook migrated past Willow Creek weir (WCW), of which an estimated 880 were harvested by anglers, yielding and escapement of 36,109 fish. The 2013 run of fall Chinook was comprised of an estimated 17,104 naturally-produced adult and 6,514 jack salmon and 13,168 hatchery-produced adults and 6,514 hatchery-produced jacks. The post-harvest escapement of 16,689 naturally-produced adult fall Chinook was 27% of the 62,000 fish TRRP goal. The coho run-size in the Trinity above Willow Creek was estimated at 21,906 fish, with no coho reported as harvested, leaving all 21,906 fish for potential spawning escapement. The coho escapement was comprised of an estimated 4,305 naturally-produced adult and 152 jack coho and 14,782 hatchery-produced adult and 2,667 hatchery-produced jacks.

coho, Chinook, Trinity
2016Pacific Fishery Management Council Klamath River Technical TeamKlamath River Fall Chinook Salmon Age-Specific Escapement, River Harvest, and Run Size Estimates, 2015 Run, , 18010209

This report describes the data and methods used by the Klamath River Technical Team (KRTT) to estimate age-specific numbers of fall Chinook salmon returning to the Basin in 2015. The estimates provided in this report are consistent with the Klamath Basin Megatable (CDFW 2016) and with the 2016 forecast of ocean stock abundance (KRTT 2016). Age-specific escapement estimates for 2016 and previous years, coupled with the coded-wire tag (CWT) recovery data from Basin hatchery stocks, allow for a cohort reconstruction of the hatchery and natural components of Klamath River fall Chinook salmon (Goldwasser et al. 2001, Mohr 2006a, KRTT 2016). Cohort reconstruction enables forecasts to be developed for the current year’s ocean stock abundance, ocean fishery contact rates, and percent of spawners expected in natural areas (KRTT 2016). These forecasts are necessary inputs to the Klamath Ocean Harvest Model (Mohr 2006b), the model used by the Pacific Fishery Management Council to forecast the effect of fisheries on Klamath River fall Chinook salmon.

Chinook, harvest
2017Klamath Basin Monitoring ProgramKlamath Basin Monitoring Program Document Library, , 180102

This is a Google Sheets list of reports and white papers primarily related to water quality as well as fish health compiled by the Klamath Basin Monitoring Program (KBMP). There are currently 322 records.

water quality, fish health, KBMP
2012Mid Klamath Watershed Council2012 Instream Candidate Actions Table for the Mid Klamath Watershed, 18010209

This Excel spreadsheet identifies and prioritizes potential specific habitat restoration projects in the Mid Klamath Watershed by tributary.

habitat restoration, coho, Chinook, steelhead
2017U.S. Fish & Wildlfie Service, Task Force membersKlamath River Basin Fisheries Task Force, , , , 18010209

This website links to the Klamath River Fisheries Task Force website. The Klamath Act expired on October 1, 2006, and was not reauthorized by Congress. The funding for this program was eliminated and the charter was discontinued. The information on this site is provided for reference. Links to prior reports and meeting minutes are available, along with the Task Force charter.

coho, Chinook, steelhead, habitat restoration
2014Agreement Signatories (State of Oregon, Klamath Tribes, water users)Upper Klamath Basin Comprehensive Agreement18010203

The Purposes of this Upper Klamath Basin Comprehensive Agreement (“Agreement”) are to achieve four co-equal goals: (a) To support the economic development interests of the Klamath Tribes; (b) To provide a stable, sustainable basis for the continuation of agriculture in the Upper Klamath Basin; (c) To manage and restore riparian corridors along streams that flow into Upper Klamath Lake in order to achieve Proper Functioning Conditions permanently; and (d) To resolve controversies regarding certain water right claims, contests, and exceptions in the ongoing Klamath Adjudication in the Klamath County Circuit Court.

water rights
2008National Fish and Wildlife FoundationDraft Business Plan for the Upper Klamath Basin, 18010203

In the context of the National Fish and Wildlife Foundation’s conservation efforts, the Upper Klamath business plan represents the strategies necessary to meet the conservation goals of Keystone and other initiatives.
The plan emphasizes the type(s) and magnitude of the benefits that will be realized through the initiative, the monetary costs involved, and the potential obstacles (risks) to achieving those gains. Each of the Foundation’s business plans has three core elements: (1) Conservation Outcomes: A concrete description of the outcomes to which the Foundation and grantees will hold ourselves accountable. (2) Implementation Plan with Strategic Priorities and Performance Measures: A description of the specific strategies that are needed to achieve our conservation outcome and the quantitative measures by which we will measure success and make it possible to
adaptively revise strategies in the face of underperformance, and (3) Funding and Resource Needs: An analysis of the financial, human and organizational resources needed to carry out these activities.
Six partners have been working together to develop and implement this Upper Klamath Basin Keystone Initiative: the Klamath Basin Rangeland Trust, the Klamath Tribes, the Klamath Watershed Partnership, the Nature Conservancy, Sustainable Northwest and the US Fish & Wildlife Service. We are in the process of integrating other natural resource agencies and organizations in the Basin, including the US Bureau of Reclamation, the USDA Natural Resource Conservation Service, the Oregon Department of Fish & Wildlife, the Klamath Soil & Water Conservation District and Ducks Unlimited. Implementation will not be limited to the listed entities. As the Business and Strategic Plans are developed, we expect other organizations will participate in both their design and execution.

Upper Klamath basin
2013National Marine Fisheries Service and U.S. Fish & Wildlife ServiceKlamath Project Biological Opinion, , , , , , , , 180102

This joint, multi-species Biological Opinion for the Klamath Project covers project operations and their impacts on ESA listed species (SONCC coho, Lost River suckers, short nose suckerrs, eulachon, and green sturgeon).

coho, suckers
2017North Coast Regional Water Quality Control BoardScott River TMDL180102

The following documents are available for the Scott River TMDL: Fact Sheet: Implementation of the Scott River TMDL Conditional Waiver of Waste Discharge Requirement Program, Scott River TMDL Conditional Waiver of Waste Discharge Requirements, Scott Valley Community Groundwater Study Plan, Scott River Watershed Water Quality Compliance and Trend Monitoring Plan, Action Plan for the Scott River Watershed Sediment and Temperature Total Maximum Daily Loads and Staff Report for the Action Plan for the Scott River Watershed Sediment and Temperature Total Maximum Daily Loads.

TMDL
2017North Coast Regional Water Quality Control BoardShasta River TMDL18010209

The purpose of this website is to provide information on the Shasta River TMDLs. The Klamath Basin TMDL Fact Sheet provides general information about Shasta and Klamath Rivers.

TMDL
2017Clayton Creager, North Coast Regional Water Quality Control BoardLower Lost River TMDL18010204

The Lost River watershed encompasses an areas of approximately 3,000 square miles in Klamath and Lake counties in Oregon, and Modoc and Siskiyou counties in California. The Upper Lost River originates in California at the outlet of Clear Lake, and flows north into Oregon, near the Malone Dame. The Lower Lost River continues downstream of Malone Dame, flowing northwest, where it receives substantial inflow from Gerber Reservoir, and then turns westward toward the Harpold Dam. Beyond the Harpold Dam, the Lower Lost River receives inflow of Klamath River water by way of the A-Canal and Lost River Diversion Channel. The Lost River Diversion Dam can also divert water to the Klamath River.

The Lower Lost River watershed is composed of two hydrologic subareas: the Tule Lake Hydrologic Sub Area and the Mt. Dome Hydrologic Sub Area.

TMDL
2017North Coast Regional Water Quality Control BoardLost River, Upper TMDL, 18010204

The Upper Lost River watershed (the Lost River upstream of the Oregon border, including Clear Lake Reservoir and tributaries) was delisted from the Section 303(d) List for nutrients and water temperature impairments in 2006, as North Coast Regional Water Quality Control Board (Regional Water Board) staff analyses concluded that the listings were not warranted. The TMDL analysis documents available are:
- Total Maximum Daily Load Analysis Water Temperature and Nutrients
- Response to Comments
- Map 1: Location of Klamath River Basin and Upper Lost River
- Map 2: Upper Lost River Modoc Plateau

TMDL, nutrients
2017Clayton Creager, North Coast Regional Water Quality Control BoardKlamath River TMDL180102

On September 7, 2010 the State Water Resources Control Board adopted a Resolution approving amendments to the Water Quality Control Plan for the North Coast Region to establish: (1) Site Specific Dissolved Oxygen Objectives for the Klamath River; (2) an Action Plan for the Klamath River Total Maximum Daily Loads Addressing Temperature, Dissolved Oxygen, Nutrient, and Microcystin Impairments in the Klamath River; and (3) an Implementation Plan for the Klamath and Lost River Basins. On December 28, 2010, the US Environmental Protection Agency approved the TMDLs for the Klamath River in California pursuant to CWA Section 303(d)(2). The TMDLs, Implementation Plan, and new Dissolved Oxygen Objectives are in effect.

TMDL, monitoring,
2002Matthew Boyd, Steve Kirk, Mike Wiltsey, Brian Kasper, DEQUpper Klamath Lake Drainage Total Maximum Daily Load (TMDL) and Water Quality Management Plan (WQMP), , 18010203

The Upper Klamath Lake drainage is comprised of three 4th field hydrologic units (i.e. the Upper Klamath Lake subbasin, the Williamson River subbasin, and the Sprague River subbasin) and has stream segments listed on the 1998 Oregon 303(d) list for: temperature, dissolved oxygen (DO), chlorophyll-a, pH, and habitat modification. The TMDL developed in this document for each of the 303(d) water quality parameters identifies pollutants and establishes loading limits designed to comply with water quality standards. Habitat and flow modification concerns are identified under biological criteria standard exceedance and will be addressed in management plans to be developed by designated management agencies (DMAs). As they are not pollutants, TMDLs will not be developed for habitat and flow modification. Chlorophyll-a is listed in the Oregon Administrative Rules (OAR) as a “nuisance criteria” and will be addressed in the Water Quality Management Plan (WQMP).

DEQ, water quality, WQMP, TMDL
2017KTAPKlamath Basin Map, , , , , , , , , , , , , , , , , 180102

Klamath map showing the various areas of the Klamath Basin.

Lower Klamath,
2017KRBKlamath River Basin PIT Tagging Database (KRB), , , 180102

The Klamath River Basin PIT Tagging Database (KRB) application is to facilitate the sharing and understanding of PIT tag data in the Klamath River Basin of Southern Oregon and Northern California.

PIT Tagging, KRB
2017PFMCPacific Fishery Management Council (PFMC), , ,

The Pacific Fishery Management Council is one of eight regional fishery management councils established by the Magnuson Fishery Conservation and Management Act of 1976.

With jurisdiction over the 317,690 square mile exclusive economic zone off Washington, Oregon and California, the Council manages fisheries for about 119 species of salmon, groundfish, coastal pelagic species (sardines, anchovies, and mackerel), and highly migratory species (tunas, sharks, and swordfish). The Council is also active in international fishery management organizations that manage fish stocks that migrate through the Council’s area of jurisdiction, including the International Pacific Halibut Commission (for Pacific halibut), the Western and Central Pacific Fisheries Commission (for albacore tuna and other highly migratory species), and the Inter-American Tropical Tuna Commission (for yellowfin tuna and other high migratory species).

Fisheries, Conservation
2017MKWCMid Klamath Watershed Council (MKWC), , , 180102

Since 2001, the Mid Klamath Watershed Council (MKWC) has been working to restore the threatened Klamath River in Northern California and the upslope habitats upon which the river depends. The Klamath River and its tributaries, including the Salmon and Trinity Rivers, have some of the largest remaining wild salmon runs in the lower 48 States and hold the promise of significant ecological improvement through restoration programs.

MKWC is a 501 (c) (3) non-profit organization formed by a diverse group of participants in 2001. Our programs in the Middle Klamath subbasin include Watershed Education, Invasive Weed Management, Roads, Fire and Fuels, Fisheries, Wildlife, Foodsheds and Native Plants. We leverage state, federal, and private grant funding, combined with community volunteerism to accomplish high-value and low-cost restoration actions throughout the Middle Klamath subbasin.

Watershed, Education, Invasive Weed Management, Fisheries, Wildlife, Foodsheds, Native Plants, Stewardship
2017USDA, United States Department of Agriculture - Forest ServiceWatershed and Fisheries Ecological Restoration on the Six Rivers National Forest, , , , , , 18010209

The Six Rivers National Forest is in the early stages of developing a project to restore aquatic habitats in selected stream reaches across the forest. The overall purpose of the restoration project is to improve riparian and instream conditions for anadromous fisheries including listed threatened and sensitive fisheries and their critical habitats. The forest is considering a suite of potential restoration actions including adding large woody debris to provide cover for juvenile coho salmon, and developing side-channel areas for winter rearing and riparian treatments to encourage species diversity.

watershed, USDA, erosion, sedimentation
2017USGSUSGS – Oregon Water Science Center, , , , , , ,

The USGS Oregon Water Science Center provides reliable water data and interpretation of data to Federal, State, and local agencies, Tribes, and the public. The data and study results are widely used to manage Oregon's water resources for the benefit of people and our environment. This Website is the gateway to a wealth of information on surface water, groundwater, and water quality in Oregon and the Nation.

USGS, groundwater, surface water, water data
2015US Fish and Wildlife ServiceArcata Fish and Wildlife Office, , , , ,

The mission of the U.S. Fish and Wildlife Service is: working with others to conserve, protect, and enhance fish, wildlife, and plants and their habitats for the continuing benefit of the American people. The Arcata Fish and Wildlife Office has several working groups, such as the Trinity River Adaptive Management Working Group.

fisheries, wildlife, conservation, endangered species,
2017ODFWOregon Department of Fish and Wildlife (ODFW), , , , , , , , , , ,

The mission of the Oregon Department of Fish and Wildlife (ODFW) is to protect and enhance Oregon's fish and wildlife and their habitats for use and enjoyment by present and future generations.

fishing, wildlife, ODFW, conservation, recovery, Oregon Lamprey
2017DEQOregon Department of Environmental Quality (DEQ), , , , , , , ,

The Oregon Department of Environmental Quality (DEQ) is a regulatory agency whose job is to protect the quality of Oregon's environment. DEQ's mission is to be a leader in restoring, maintaining and enhancing the quality of Oregon's air, land and water. DEQ works collaboratively with Oregonians for a healthy, sustainable environment.

DEQ, air quality, water quality
2017State of California - California Department of Fish and WildlifeCalifornia Department of Fish and Wildlife, , , , ,

The California Department of Fish and Wildlife’s (CDFW), formerly known as the California Department of Fish and Game (CDFG), is a state agency under the California Natural Resources Agency. The Department of Fish and Wildlife manages and protects the state's fish, wildlife, plant and native habitats. It is responsible for related recreational, commercial, scientific, and educational uses. It also works to prevent illegal poaching. The site links to a Document Library that is an online repository of thousands of documents.

conservation, fishing, water policy, wildlife, CDFW
2017NOAAPacific Coastal Salmon Recovery Fund (PCSRF), , ,

Pacific salmon and steelhead are much more than essential elements of a healthy Pacific Coast ecosystem; they are cultural icons woven into the fabric of local communities and economies. Salmon runs tie the region's people to the landscape, but pressures from a changing environment and human activities have compromised the strength of these runs. The Pacific Coastal Salmon Recovery Fund (PCSRF) was established by Congress in 2000 to reverse the declines of Pacific salmon and steelhead, supporting conservation efforts in California, Oregon, Washington, Idaho, and Alaska. The program is essential to preventing the extinction of the 28 listed salmon and steelhead species on the West Coast and, in many cases, has stabilized the populations and contributed to their recovery course.

recovery fund, PCSRF, NOAA
2017NOAANOAA – West Coast Region – Klamath River Basin, , , , , , 180102

The Reclamation Act of 1902 (43 U.S.C. 391 et seq.) authorized the Secretary of the Interior to locate, construct, operate, and maintain works for the storage, diversion, and development of water for the reclamation of arid and semiarid lands in the western States. The headwaters of the Klamath River originate in Southern Oregon and flow through the Cascade Mountain Range to the Pacific Ocean south of Crescent City, California. The river extends nearly 250 miles and is just one of three waterways that pass through the Cascades to the Pacific. It is named after a native American name - klamet - meaning swiftness.

The Klamath River Basin supports Chinook salmon, coho salmon, and steelhead populations, among other anadromous species. Historically, anadromous fish populations supported important commercial, recreational, and tribal fisheries. However, many anadromous fish populations have declined substantially in abundance. Restoration of these populations will require strong partnerships and collaboration between agencies and stakeholders throughout the basin. Links to reports and document in three main areas: water management, hydroelectric management, and salmon management,

coho salmon, chinook salmon, anadromous fish
2014Julie Weeder, NOAANOAA – Southern Oregon Northern California Coast Coho Salmon Recovery Plan (SONCC), , , 180102

NOAA Fisheries released the final Southern Oregon/Northern California Coast (SONCC) Coho Salmon Recovery Plan on September 30, 2014. The goal of the plan is to restore SONCC coho salmon to healthy, self-sustaining numbers so that the protections of the Endangered Species Act are no longer necessary. Conservation partners have advanced many habitat restoration, barrier removal, and threat reduction actions since the species was listed in 1997, and the plan was developed with extensive input from these partners. The recovery plan provides a means to organize and coordinate recovery of this species based on the best available scientific information.

NOAA, SONCC, spawning habitat, coho salmon
2017North Coast Regional Water Quality Control BoardNorth Coast Regional Water Quality Control Board Basin Plan,

Water quality control plans (North Coast Regional Water Quality Control Board Basin Plan) provide the basis for protecting water quality in California. Basin Plans are mandated by both the Federal Clean Water Act (CWA) and the State Porter-Cologne Water Quality Act (Porter-Cologne). Sections 13240-13247 of Porter-Cologne specify the required contents of a regional basin plan.

The Basin Plan is the Regional Water Board's master water quality control planning document. It designates beneficial uses and water quality objectives for waters of the State, including surface waters and groundwater. It also includes programs of implementation to achieve water quality objectives. The Basin Plan has been adopted and approved by the State Water Resources Control Board (State Board), as well as by the United States Environmental Protection Agency (USEPA) and the Office of Administrative Law (OAL) when required.

water protection, CWA,
2017The Klamath TribesThe Klamath Tribes, , , , , , , , , 180102

The Klamath, Modoc, and Yahooskin Mission Statement.

“The mission of the Klamath Tribes is to protect, preserve and enhance the spiritual, cultural and physical values and resources of the Klamath, Modoc and Yahooskin Peoples by maintaining the customs and heritage of our ancestors. To establish comprehensive unity by fostering the enhancement of spiritual and cultural values through a government whose function is to protect the human and cultural resources, treaty rights, and to provide for the development and delivery of social and economic opportunities for our People through effective leadership.”

customs, heritage, treaty rights, agreements
2016USGSUSGS – Klamath Falls Field Station, , , , , , , , , , , 18010203

The primary mission of the Klamath Falls Field Station (KFFS) is to conduct rigorous scientific investigations into issues related to the management and recovery of endangered Lost River and shortnose sucker populations in the Upper Klamath Basin. Populations of these species exist in a number of water bodies within the Basin, but the primary populations of interest are those located in Upper Klamath Lake (Oregon) and Clear Lake Reservoir (California). Upper Klamath Lake has become hypereutrophic due to changes in land-use practices, and poor water quality in the summer and fall appears to play a role in limiting the recovery of endangered sucker populations. Clear Lake Reservoir has also been affected by land-use changes and water management in the Upper Basin, and populations of suckers in this reservoir are receiving increasing attention. The KFFS conducts research related to all life stages of the suckers and maintains a substantial field sampling program that lends itself to collaborative investigations. A major element of KFFS research is a long-term capture-recapture monitoring program for adult suckers that uses PIT tags and remote detection systems. The sampling and data analysis expertise of the KFFS has proven to be transferrable to a variety of other species of interest, most recently for projects related to salmonids being conducted jointly with other federal and state agencies and tribes.

KFFS, Shortnose suckers
2016U.S. Fish & Wildlife ServiceU.S. Fish and Wildlife Service – Lower Klamath National Wildlife Refuge, , 18010209

The National Wildlife Refuge System, within the U.S. Fish and Wildlife Service, manages a national network of lands and waters set aside to conserve America’s fish, wildlife, and plants. The Final Comprehensive Conservation Plan for the Klamath Basin National Wildlife Refuges is above on the website.

resource management, conservation
2016US Fish and Wildlife ServiceKlamath Falls Fish and Wildlife Office, , , , 18010203

Within the Upper Klamath Basin, conservation efforts are coordinated by the Klamath Falls Fish and Wildlife Office through the voluntary cooperation and participation of a variety of agencies, organizations, private landowners, and individuals. Conservation efforts to maintain and restore the function and health of the Upper Klamath Basin ecosystem are supported and facilitated through USFWS-sponsored activities including;

- Protecting and restoring animals and plants that are in danger of extinction both in the United States and worldwide.
- Providing expert biological advice to other Federal agencies, states, industry, and members of the public concerning the conservation of fish and wildlife habitats that may be affected by development activities.
- Administering Federal grant money to support specific projects carried out by state fish and wildlife agencies.
- Working private landowners and others to conserve and restore habitat on private lands.

outreach, education, suckers
2016Yurok TribeThe Yurok Tribe, , , 180102

The mission of the Yurok Tribe is to exercise the aboriginal and sovereign rights of the Yurok People to continue forever our Tribal traditions of self-governance, cultural and spiritual preservation, stewardship of Yurok lands, waters and other natural endowments, balanced social and economic development, peace and reciprocity, and respect for the dignity and individual rights of all persons living within the jurisdiction of the Yurok Tribe, while honoring our Creator, our ancestors and our descendants.

self-governance, stewardship
2017Trinity River Restoration ProgramTrinity River Restoration Program (TRRP), ,

TRRP is a multi-agency program with eight Partners forming as the Trinity Management Council (TMC), plus numerous other collaborators. The main office is located in Weaverville, CA (contact) although various Partner offices include staff working in the program.Primary components are TMC (Trinity Management Council) – acts much like a Board of Directors. Agencies with membership are frequently referred to as the “TRRP Partners”.
TAMWG (Trinity Adaptive Management Working Group) – provides stakeholder/public oversight. SAB (Science Advisory Board) – a group of independent scientists. TRRP Staff – employees of TRRP Partner agencies and their representatives. Work Groups – discipline-oriented committees to resolve technical matters.

TRRP
2017Restoration Agreement signatoriesKlamath Restoration Agreements – Restoring a River and Revitalizing Communities, , , , 180102

On May 21, 2014 Senator Ron Wyden introduced the Klamath Water Recover and Economic Restoration Act. The legislation would implement the terms of the three Klamath Restoration Agreements: the Klamath Basin Restoration Act, Klamath Hydroelectric Settlement Agreement, and Upper Basin Comprehensive Agreement.

agreement, KHSA, KBRA
2017Scott River Watershed CouncilScott River Watershed Council, 18010209

Originally established in 1992, the SRWC became a nonprofit in 2011. We cooperatively seek solutions to enhance local resources and facilitate community collaboration on watershed issues. SRWC provides leadership to support science-based restoration in Scott Valley. SRWC brings research, education and discussion on natural resource issues to the community, and implements restoration projects based on community and ecosystem needs.

watershed, SRWC, restoration
2015Klamath Tribal Water Quality ConsortiumKlamath Tribal Water Quality Consortium – http://www.klamathwaterquality.com/, , 18010209

Welcome to the Klamath Tribal Water Quality Consortium (formerly known as the Klamath Basin Tribal Water Quality Work Group) website, which is designed to inform the public about Klamath River water quality problems and how to solve them. The Consortium, made up of leaders of five Tribal water quality or environmental departments, collaborates on larger basin-scale water quality issues such as Klamath Hydroelectric Project (KHP) and Clean Water Act implementation (TMDL). Other regulatory processes relevant to water quality, such California Department of Fish and Game Incidental Take Permits (ITP) for coho salmon, are also discussed on this site.

The Consortium participants have conducted numerous complex scientific investigations concerning Klamath River water quality impairment since the group’s inception in 2003. This website presents Tribal studies, as well as continuing scientific discoveries by agencies, academic institutions and non-governmental organizations (see new science). It also provides a portal for tracking important governmental and regulatory processes that affect Klamath River water quality, fisheries and Tribal Trust resources.

KHP, TMDL
2017Klamath Tracking and Accounting Program (KTAP)Klamath Tracking and Accounting Program (KTAP), , , , , , , , , , , 180102

Klamath Tracking and Accounting Program (KTAP) is a local program seeking to better understand the benefits to water quality created by changes in land management and restoration projects. KTAP seeks to highlight the collective benefit that restoration and land management projects provide for water quality and habitat for native fish in the Klamath Basin. KTAP Stewardship Project Reporting Protocol defines a consistent system to track voluntary conservation and restoration actions in a way that 1) enables local practitioners and funders to make informed decisions regarding where and how to invest in water quality and habitat improvement; 2) provide the basis for scientific research that furthers our understanding of the system.

KTAP, watershed health
2017National Fish and Wildlife FoundationKlamath River Coho Enhancement Fund, , , , , , , 180102

The Klamath River, which runs through southern Oregon and the northern Californian coast, was once the third most productive salmon river system in the United States. Currently, the Southern Oregon/Northern California Coast (SONCC) coho salmon, native to the Klamath River, is listed as threatened under both California and federal Endangered Species Acts due to issues stemming from dammed water, flow variability, and water pollution. This program is a conservation partnership between NFWF and PacifiCorp Energy to assist PacifiCorp in meeting the environmental commitments in its Habitat Conservation Plan for Coho Salmon. In most cases, projects funded under this project also support NFWF's Lower Klamath Basin conservation priorities.

Endangered Species Acts, SONCC, coho salmon, spawning habitat,
2017Ed SheetsEd Sheets Consulting – Facilitation, Mediation, and Energy and Natural Resource Analysis, , , , , , 180102

Facilitation and Mediation, Energy and Natural Resource Analysis. Ed Sheets has over 39 years of experience working to build consensus with a broad range of organizations. He has worked as an independent consultant for 20 years, focusing on facilitating and mediating complex natural resource disputes and providing energy and natural resource analysis. He also worked to resolve complex issues in his positions as executive director of the Northwest Power and Conservation Council, director of the Washington State Energy Office, and as special assistant to the late United States Senator Warren Magnuson.

Facilitation, Mediation, Energy, Natural Resource Analysis, KHSA, UKBCA, KBRA
2017Klamath Basin Monitoring ProgramKlamath Basin Monitoring Program (KBMP), , , , , , , 180102

The Klamath Basin Monitoring Program facilitates the coordination and implementation of water quality monitoring in support of the stewardship, protection, and restoration of all beneficial uses within the Klamath River watershed, with the ultimate goal of restoring water quality. Over the past decade, the Klamath Basin has been in the forefront of national attention due to contentious resource issues related to water allocation, water quality, proposed dam removal, and protection and recovery of threatened and endangered species. While many resource issues face the Klamath Basin, water quality remains at the forefront of concern for the Klamath Basin Monitoring Program (KBMP). Many diverse and discrete parties conduct monitoring in the Klamath River Basin including state and federal agencies, tribal entities, PacifiCorp, and watershed groups. The Klamath Basin Monitoring Program is comprised of many of these organizations, working together to understand and improve water quality conditions in the Klamath Basin. KBMP strives to implement, coordinate and collaborate on water quality monitoring and research throughout the Klamath Basin. KBMP monitoring activities focus on characterizing sources of impairment through the study of ecosystem elements, including water quality, fish populations and health, flows, benthos, and aquatic plant communities. KBMP monitoring aids the development and implementation of Total Maximum Daily Load (TMDL) plans by monitoring loadings basin wide. KBMP monitoring also informs the public and tribal community of public health concerns. KBMP members host two annual meetings aimed at addressing water quality concerns basin wide. Membership to the KBMP is voluntary, as are the KBMP committees.

KBMP, spawning habitat, iron gate hatchery,
2017Official U.S. Department of the InteriorKlamath Basin Water Issues – klamathrestoration.gov, , , , , , , 180102

This is the official website of the Department of the Interior, and other federal and state agencies that are involved in carrying out obligations set forth in the Klamath Hydroelectric Settlement Agreement (KHSA), including the Secretarial Determination on Klamath River dams. Use this website to stay up to date on issues surrounding the Secretarial Determination and the environmental analysis that will be conducted pursuant to the National Environmental Policy Act (NEPA) and the California Environmental Quality Act (CEQA).

KHSA, NEPA, CEQA, Restoration, Agreements
2008T. Beechie, G. Pess, P. Roni, G GiannicoSetting River Restoration Priorities: a Review of Approaches and a General Protocol for Identifying and Prioritizing Actions, , , , ,

Implicit in the question, ‘‘How should I prioritize restoration actions?’’ is often the unstated question, ‘‘What should I restore?’’ Distinguishing between these questions helps clarify the restoration planning process, which has four distinct steps: (1) identify the restoration goal, (2) select a project prioritization approach that is consistent with the goal, (3) use watershed assessments to identify restoration actions, and (4) prioritize the list of actions. A well-crafted restoration goal identifies the biological objective of restoration, addresses underlying causes of habitat change, and recognizes that social, economic, and land use objectives may constrain restoration options. Once restoration goals are identified, one of six general approaches can be selected for prioritizing restoration actions: project type, refugia, decision support systems, single-species analysis, multispecies analysis, and cost effectiveness. Prioritizing by project type, refugia, or a decision support system requires the least quantitative information, and each approach is relatively easy to use. Single-species, multispecies, and cost effectiveness approaches require more information and effort but often most directly address legal requirements. Watershed assessments provide most of the information used to identify and prioritize actions and should be explicitly and carefully designed to support the goals and prioritization scheme. Watershed assessments identify causes of habitat degradation, habitat losses with the greatest effect on biota and ecosystems, and local land and water uses that may limit restoration opportunities. Results of assessments are translated into suites of restoration options, and analysis of land use and economic constraints helps to evaluate the feasibility of various options. Finally, actions are prioritized based on assessment results and the selected prioritization scheme.

Restoration, land use, habitat conditions, biological responses
2010KHSAKlamath Hydroelectric Settlement Agreement (KHSA), , 180102

The Parties have entered into this Settlement for the purpose of resolving among them the pending FERC relicensing proceeding by establishing a process for potential Facilities Removal and operation of the Project until that time.

settlement, KWAPA, UKWUA, FERC
2016LeRoy Poff, John C. SchmidtHow Dams Can Go with the Flow,

Dams alter flow, sediment, and thermal regimes of rivers. Seasonal flow distortions(top) cause shifts in species compositions. Dammed rivers with hydropeaking cause daily distortions that can eliminate key species from food webs. Small changes to flow releases can counteract these distortions and provide ecological benefit.

Post-dam environmental flow management can only incrementally improve lost ecosystem functions, making predam environmental planning essential. Making hydropower greener and dams more sustainable generally requires not only better design and management of flow releases but also balancing economic gain against environmental degradation and human dislocations, all in an increasingly uncertain hydrologic future.

2011CDMKlamath Settlement Process Sediment Management in the Reservoirs, , 180102

The United States Department of the Interior (DOI), as the National Environmental Policy Act (NEPA) lead agency, and the California Department of Fish and Game (DFG), as the California Environmental Quality Act (CEQA) lead agency, are currently developing an Environmental Impact Statement/ Environmental Impact Report (EIS/EIR) for the Klamath Hydroelectric Settlement Agreement (KHSA) and the Klamath Basin Restoration Agreement (KBRA). The EIS/EIR will evaluate the environmental and social effects of a set of alternatives that may include removing all or portions of four dams on the Klamath River providing volitional fish passage to aid in restoring salmonid fisheries.

KBRA, KHRA, Iron Gate Reservoir, Cultural Sites
2011Scott Wright, River Design GroupFeasibility, Risk and Uncertainty of Mechanical Sediment Removal with the Proposed Action (Full Facility Removal), , , , , 180102

The United States Department of the Interior (DOI), as the National Environmental Policy Act (NEPA) lead agency, and the California Department of Fish and Game (DFG), as the California Environmental Quality Act (CEQA) lead agency, are currently developing an Environmental Impact Statement/ Environmental Impact Report (EIS/EIR) for the Klamath Hydroelectric Settlement Agreement (KHSA) and the Klamath Basin Restoration Agreement (KBRA). The EIS/EIR will evaluate the environmental and social effects of a set of alternatives that may include removing all or portions of four dams on the Klamath River in order to provide volitional fish passage to aid in restoring salmonid fisheries. The Proposed Action, as defined in the EIS/EIR, is full facilities removal of four dams with controlled sediment erosion and downstream transport.

The KHSA stipulates that a determination must be made by the U.S. Secretary of the Interior regarding whether removal of the four dams will enhance salmonid fisheries and will be in the public interest. The four dams are J.C. Boyle, Copco 1, Copco 2, and Iron Gate dams. Three of the reservoirs created by the dams (J.C. Boyle, Copco 1, and Iron Gate) have accumulated large amounts of sediment over time. Under the provisions of the KHSA, the sediment would be naturally eroded and released to the Klamath River with dam removal. The EIS/EIR will address the effects to the aquatic resources from the release of sediment to the downstream river.

Mechanical removal of sediment from the reservoirs, prior to and during dam removal, could help mitigate or reduce downstream impacts to aquatic resources and water quality in the Klamath River. The purpose of this technical memorandum is to briefly summarize the holistic effects and risks associated with mechanical removal of potentially erodible reservoir sediments. This technical memorandum is primarily a synthesis of other reports and information available in the EIS/EIR document.

KBRA, KHSA, sediment, fall chinook, spring chinook, pacific lamprey, coho salmon
2011ReclamationDetailed Plan for Dam Removal – Klamath River Dams, , , , 180102

The Klamath Hydroelectric Project (Project) is owned by PacifiCorp, and includes four generating developments along the mainstem of the Upper Klamath River between river mile (RM) 190 and 228. The East Side and West Side Developments are located further upstream at the Bureau of Reclamation’s (Reclamation’s) Link River Dam at RM 254, and have been previously proposed by PacifiCorp for decommissioning. The Project also includes a re-regulation dam with no generation facilities at RM 233 (Keno Dam), and a small (2.2 MW) generating development on Fall Creek, a tributary to the Klamath River at RM 196.3. The installed generating capacity of the existing Project is 169 MW and, on average, the Project generates 716,800 MWh of electricity annually. PacifiCorp began relicensing proceedings before the Federal Energy Regulatory Commission (FERC) in 2000.

iron gate hatchery,
2011ReclamationHydrology, Hydraulics, and Sediment Transport Studies for the Secretary’s Determination on Klamath River Dam Removal and Basin Restoration., , , , 180102

The surface hydrology, groundwater hydrology, hydraulics, geomorphology, and sediment transport of the Klamath River Basin are analyzed as they pertain to the No Action and Dam Removal Alternatives of the Secretarial Determination on Klamath Dam Removal and Basin Restoration. The studies summarized in this document are consistent with those identified in the Project Management Plan for the Secretarial Determination on Klamath Dam Removal and Basin Restoration (PMP). The studies are intended to address the effects of the Klamath Basin Restoration Agreement (KBRA) and the Klamath Hydroelectric Settlement Agreement (KHSA).

KBRA, KHSA, PMP
2012DOIAssessment of Potential Changes to Real Estate Resulting from Dam Removal: Klamath Secretarial Determination Regarding Potential Removal of the Lower Four Dams on the Klamath River18010209

This study is in support of the Secretarial Determination on the removal of four dams on the Klamath River and related restoration activities in the Klamath basin. The four dams are Copco I, Copco II, J.C. Boyle and Iron Gate. Lands under these reservoirs and adjacent lands associated with the hydroloelectric project and owned by PacifiCorp are to be transferred to the states of Oregon and California or an entity yet to be determined. Lands adjacent to Keno Dam presently owned by PacifiCorp are to be transferred to the Department of Interior to support the continued operation of the Keno dam and impoundment. All of these lands are described in the Klamath Hydroloelectric Settlement Agreement (KHSA) as Parcel B lands and represent approximately 8000 acres of property owned by PacifiCorp. These lands are to be managed for public interest purposes such as fish and wildlife habitat restoration, public education, and public recreational purposes as outlined in section 7.6.4 of the KHSA. Lands adjacent to Keno Impoundment are intended to support the continued operation of Keno Impoundment for the Klamath Project.

Real Estate, Iron Gate Dam
2012BRIDam Removal Real Estate Evaluation Report180102

The purpose of this assignment is to determine the impacts to the value of the real property of those impacted parcels that align and/or are influenced by the reservoirs that have formed behind the three identified dams. The client is the Office of Valuation Services and the intended user is the Department of the Interior. The report is intended to be used by the Realty Sub-team, as input to the NEPA Team, in connection with the Environmental Impact Statement being prepared on the potential removal of the four identified dams.

Real Estate, Iron Gate Dam
2011Water Quality Sub TeamAssessment of Long Term Water Quality Changes for the Klamath River Basin Resulting from KHSA, KBRA, and TMDL and NPS Reduction Programs, , 180102

This assessment, prepared by the Water Quality Sub Team (WQST) in support of the Secretarial Determination for the Klamath Hydroelectric Settlement Agreement (KSHA) process, qualitatively considers anticipated water quality effects in the Klamath Basin under the No Action and the Proposed Action alternatives. Under the Proposed Action Alternative (positive determination for dam removal), anticipated restoration measures related to KSHA and the Klamath Basin Restoration Agreement (KBRA) are considered, with regard to pace and potential for achieving water quality improvements. The primary purpose of this assessment is to discern the relative impacts of the Proposed Action as compared with the No Action alternative, including how these actions may interact with existing and proposed Total Maximum Daily Load (TMDL) implementation efforts and other ongoing water quality related programs in the Klamath Basin. The assessment represents the most comprehensive consideration to date of potential water quality related actions under KHSA and KBRA that would either directly or indirectly affect water quality in the Klamath Basin.

KHSA, KBRA, TMDL, NPS
2011Stillwater SciencesModel Development and Estimation of Short-term Impacts of Dam Removal on Dissolved Oxygen in the Klamath River, , 180102

This report summarizes modeling approaches, assumptions and results of a modeling evaluation of short-term variations in dissolved oxygen (DO) due to sediment releases associated with the removal of one or more of four dams in the Klamath Hydroelectric Project (Figure 1; FERC Project No. 2082). Estimates of the volume of sediment retained by these dams include 10.0 million m3 (13.1 million yd3) (Greimann et al. 2011), 11.1 million m3 (14.5 million yd3) (Eilers and Gubala 2003), and 11.1 million m3 to 15.6 million m3 (14.5 to 20.4 million yd3) (GEC 2006), with a high proportion of fine sediments, organic matter, and nutrients (Shannon & Wilson, Inc. 2006). Sediment transport modeling of the impacts of dam removal on suspended sediment in the lower Klamath River indicates high short-term concentrations of suspended material (i.e., peak values of 9,000–13,600 mg/L) may occur immediately downstream of Iron Gate Dam for 2–3 months following reservoir drawdown under the Proposed Action (Greimann et al. 2011, Stillwater Sciences 2008). Using a combination of in situ sampling of sediments and water quality, combined with numerical modeling, this study was developed to estimate the potential influences that re-suspension of reservoir deposits may have on DO levels in the Klamath River downstream of the dams. A numerical model was developed to help in understanding these dynamics, using approaches similar to those described in USEPA (1985, 1987).

oxygen demand
2010ReclamationQuality Assurance Project Plan– Sediment Contaminant Study, Klamath River Sediment Sampling Program, , 180102

This Quality Assurance Project Plan documents the sampling design and quality assurance guidelines for the Sediment Contaminant Study, Klamath River Sediment Sampling Program. The study is being undertaken to inform the 2012 Secretarial Decision to either remove or retain four Klamath River dams: JC Boyle, Copco 1, Copco 2 and Iron Gate. In conjunction with toxicity studies, chemical, physical and biological analyses will help determine whether constituents may be present at harmful concentrations. This contaminant investigation will help evaluate the potential for exposing or transporting contaminated sediment should the dams be removed.

Sediment Contamination
2007KBRASummary of the Klamath Basin Restoration Agreement, , 180102

This document summarizes the early (proposed) Klamath Basin Restoration Agreement. The Agreement is intended to result in effective and durable solutions which: 1) in concert with the removal of four dams, will restore and sustain natural production and provide for full participation in ocean and river harvest opportunities of fish species throughout the Klamath Basin; 2) establish reliable water and power supplies which sustain agricultural uses, communities, and National Wildlife Refuges; and 3) contribute to the public welfare and the sustainability of all Klamath Basin communities.

KBRA
2010KBRA settlement parties, U.S. Department of the InteriorKlamath Basin Restoration Agreement for the Sustainability of Public and Trust Resources and Affected Communities (KBRA), , 180102

Final signed copy of the Klamath Basin Restoration Agreement.

KBRA
2011CDMScreening-Level Evaluation of Contaminants in Sediments from Three Reservoirs and the Estuary of the Klamath River, 2009-2011, , , , 180102

The purpose of this report is to inform the Department of Interior Secretarial Determination process regarding the potential for adverse ecological or human health effects from chemical contamination in Klamath Reservoir sediments. It evaluates if the dams are removed and a portion of the accumulated sediments is flushed downstream (Proposed Action or “dams removed”) or if the dams remain in place (No Action or “dams in”). The report does not include an evaluation of the physical effects associated with the Proposed Action. This report is only intended to provide a screening-level evaluation to inform the Secretarial Determination. A stepwise process based on the Sediment Evaluation Framework (SEF) was applied that evaluated sediment and elutriate chemistry, laboratory bioassays, bioaccumulation studies, and tissue of fish from the reservoirs. This process generated multiple lines of evidence that were compared to five relevant exposure pathways of biota and human receptors to identify potential adverse effects. The results of this evaluation suggest the Klamath Reservoir sediments can be considered relatively clean, with no chemicals present at levels that would preclude their release into downstream or marine environments. Accordingly Klamath Reservoir sediments are expected to pose no adverse effects, limited effects, or minor effects under the five exposure pathways under the Proposed Action and No Action alternatives. In the future, if there is an affirmative decision, efforts would begin to develop detailed plans for dam removal and permitting processes.

suspended sediment
2007U. S. Fish and Wildife ServiceKlamath River Fish Habitat Restoration Program18010209

This is a one-page overview of the Klamath River Fish Habitat Program, highlighting the program's background, design, accomplishments to date, and status.

coho salmon, chinook salmon, steelhead, lamprey, sturgeon, habitat restoration
2011Laura Benninger, Julie Eldredge, G. Chris HoldrenSediment Chemistry Investigation: Sampling, Analysis, and Quality Assurance Findings for Klamath River Reservoirs and Estuary, October 2009 – January 2010. In Support of the Secretarial Determination on Klamath River Dam Removal and Basin Restoration, Klamath River, Oregon and California., , , 180102

The results of the sediment studies reported in this document are part of a series of studies designed to support the Secretarial Determination on Klamath Dam Removal and Basin Restoration in support of the Klamath Hydroelectric Settlement Agreement (KHSA) and the Klamath Basin Restoration Agreement (KBRA). The primary goal of this study was to provide quantitative estimates of the concentrations and distribution of potentially toxic compounds contained within sediment currently trapped behind the four PacifiCorp dams being considered for removal under the KHSA. Elutriate analyses further allow for estimation of the concentrations of chemicals that are likely to be released to the water column should reservoir sediments become suspended or transported through facilities removal.

suspended sediment
2012U.S. Department of the Interior, California Department of Fish and GameFinal Klamath Facilities Removal Environmental Impact Statement/Environmental Impact Report/Environmental Impact Statement180102

This Klamath Facilities Removal Environmental Impact Statement/Environmental Impact Report (EIS/EIR) evaluates the potential impacts of the removal of the four PacifiCorp1 dams on the Klamath River as contemplated in the Klamath Hydroelectric Settlement Agreement (KHSA). The Klamath Basin Restoration Agreement (KBRA), as well as the transfer of Keno Dam, will be treated and analyzed as a connected action. Together, these two agreements attempt to resolve long-standing conflicts in the Klamath River Basin, located in southern Oregon and northern California. The KHSA and KBRA provide for the restoration of native fisheries and sustainable water supplies throughout the Klamath River Basin. Specifically, the KHSA established a process for a Secretarial Determination. This process includes studies, environmental review, and a decision by the Secretary of the Interior regarding whether removal of J.C. Boyle, Copco 1, Copco 2, and Iron Gate Dams (1) will advance restoration of salmonid (salmon, steelhead, and trout) fisheries of the Klamath Basin, and (2) is in the public interest, which includes but is not limited to, consideration of potential impacts on affected local communities and Tribes.

This EIS/EIR has been prepared according to requirements of the National Environmental Policy Act (NEPA) and the California Environmental Quality Act (CEQA). Direct, indirect, and cumulative impacts resulting from the project alternatives on the physical, natural, and socioeconomic environment of the region are addressed.

dam removal, KHSA
2011Dr. Daniel Goodman, Dr. Mike Harvey, Dr. Robert Hughes, Dr. Wim Kimmerer, Dr. Kenneth Rose, Dr. Greg RuggeroneScientific Assessment of Two Dam Removal Alternatives on Chinook Salmon, , , , , 180102

The Secretary of the Department of the Interior is required to decide if implementation of the Klamath Hydropower Settlement Agreement (KHSA) and Klamath Basin Restoration Agreement (KBRA): (1) will advance restoration of the salmonid fisheries of the Klamath Basin; and (2) is in the public interest. There are two alternative management scenarios before the Secretary of the Interior that must be addressed in the Secretarial Determination: (1) Conditions with the lower four dams on the Klamath River in place and ongoing programs under existing laws and regulation, also referred to herein as the “Current Conditions”; and, (2) Removal of the lower four dams on the Klamath River and implementation of KBRA, also referred to herein as the “Proposed Action”.

The Panel reviewed the ongoing Chinook salmon life cycle modeling efforts and concluded that this effort was off to a promising start, but with considerable work yet to be done. If sufficient high quality data are acquired, and the modeling is completed and implemented successfully, such modeling could calculate the probabilities at which the Panel chose not to estimate. The Panel offers specific comments to improve the development and implementation of the life cycle modeling

Chinook Salmon
2011Hamilton, J., D. Rondorf, M. Hampton, R. Quiñones, J. Simondet, T. SmithSynthesis of the Effects to Fish Species of Two Management Scenarios for the Secretarial Determination on Removal of the Lower Four Dams on the Klamath River, , , , , , , 180102

In this report, we summarize anticipated effects to fish resources under two management scenarios: 1) current conditions with dams in place and without the programs and actions in the Klamath Basin Restoration Agreement (KBRA), and 2) removal of the lower four dams plus programs and actions called for in the KBRA and KHSA. This information will aid the Secretary of the Interior in determining whether dam removal and implementation of KBRA will advance restoration of salmonid (salmon and trout) fisheries. Species viability would improve for most native anadromous and resident species with dam removal and KBRA implementation. Impacts to federally listed suckers from dam removal would be minimal because reservoirs contribute little to recovery of the species; however, suckers may benefit from improved water quality in the upper basin, and specifically in Upper Klamath Lake, from the programs and actions in KBRA. Salmon fisheries would likely benefit from dam removal coastwide, since the abundances of Klamath River salmon would be less likely to reach levels that restrict commercial fishing through weak-stock management.

dam removal, coho salmon, chinook salmon, suckers, resident fish
2010John HefnerIndependent Peer Review of the Effects of Two Management Scenarios for the Secretarial Determination on Removal of the Lower Four Dams on the Klamath River180102

This memorandum presents a summary of the major comments submitted to PBS&J by two independent peer reviewers on the Effects of Two Management Scenarios for the Secretarial Determination on Removal of the Lower Four Dams on the Klamath River (July 16, 2010). Details comments are also provided, as are complete reviews. The reviewer's resumes are included in Attachment C.

dam removal
2011Dr. Thomas Dunne, Dr. Thomas Dunne, Dr. Daniel Goodman, Dr. Kenneth Rose, Dr. Kenneth Rose, Dr. Kenneth RoseKlamath River Expert Panel Final Report: Scientific Assessment of Two Dam Removal Alternatives on Coho Salmon and Steelhead, , 180102

Executive Summary The Secretary of the Department of the Interior is required to decide if implementation of the Klamath Hydropower Settlement Agreement (KHSA) and Klamath Basin Restoration
Agreement (KBRA) (1) will advance restoration of the salmonid fisheries of the Klamath Basin; and 2) is in the public interest. Two alternative management scenarios before the Secretary of
the Interior must be addressed in the Secretarial Determination: (1) Conditions with dams, also referred to herein as the “Current Conditions”; and, (2) Conditions without dams and with the KBRA, also referred to herein as the “Proposed Action.” This expert panel (Panel) was convened to attempt to answer a provided list of specific questions that had been formulated to distinguish between the effects of the two alternatives (Current Conditions and the Proposed Action) on coho salmon (Oncorhynchus kisutch) and steelhead (Oncorhynchus mykiss). Coho salmon in the Klamath River Basin are included in the Southern Oregon/Northern California
Coast Evolutionary Significant Unit (SONCC ESU) and were federally listed as threatened under the Endangered Species Act on May 6, 1997 (62 FR 24588). Report summarizes process of the expert panel, findings, and notations of any limitations based on data gaps and other factors.

dam removal, coho salmon, chinook salmon
2010Dr. David Close, Dr. Margaret Docker, Dr. Thomas Dunne, Dr. Greg RuggeroneKlamath River Expert Panel Final Report: Scientific Assessment of Two Dam Removal Alternatives on Lamprey, 180102

The expert panels are expected to provide opinions to the Secretary on the effects of the two management scenarios on fish populations. This review focuses on lamprey only. It is anticipated that these reports may
also be used for National Environmental Policy Act (NEPA) and California Environmental Quality Act (CEQA) documents generated for the KHSA and KBRA. Consequently, four expert panels were created to address native fish issues as they are impacted by the two alternative scenarios. Report summarizes the panel's process, findings, and identified limitations (data gaps).

dam removal, lamprey
2011David Buchanan, Mark Buettner, Dr. Thomas Dunne, Dr. Greg RuggeroneKlamath River Expert Panel Final Report: Scientific Assessment of Two Dam Removal Alternatives on Resident Fish, , , 180102

Summarizes the processes and findings of the Expert Review Panel on suckers, redband/rainbow trout, and bull trout. The Expert Review Panel was convened to support the Secretarial Determination process. The report summarizes the information considered and identifies outstanding information gaps.

resident fish, suckers, redband trout, rainbow trout, bull trout
2011J. S. Foott, J. L. Bartholomew, R. W. Perry, and C. E. WalkerConceptual Model for Disease Effects in the Klamath River180102

This summary report describes a conceptual model for myxozoan disease effects on juvenile Chinook and coho salmon in the Klamath River under the scenarios of current conditions and removal of the four Klamath project dams. For reasons summarized in a previous document “Compilation of Information Relating to Myxozoan Disease Effects to Inform the Klamath Basin Restoration Agreement (Compilation Report; Bartholomew
and Foott 2010), we use Ceratomyxa shasta infection as an indicator of disease mortality. A review of the parasite life cycle, parasite distribution in the Klamath River, assumptions, definitions and assessments of how specific physical and biological parameters affect disease is presented in that document. That report also prioritized the factors we believe are most important for predicting where disease effects will occur under current conditions and where future areas of high infection might occur.

fish disease, C. shasta, dam removal, chinook salmon, coho salmon
2011Stillwater SciencesKlamath Dam Removal Drawdown Scenario 8: Potential Impacts of Suspended Sediments on Focal Fish Species with and without Mechanical Sediment Removal, , Removal of four dams from the mainstem Klamath River depends on a cost-benefit

Sediment transport modeling of the impacts of dam removal on suspended sediments in the lower Klamath River indicates high short-term loads immediately downstream of Iron Gate Dam under the Proposed Action (Greimann et al. 2010, Stillwater Sciences 2008), where the latter is defined as the full removal of all four dams. The potential effects of the Proposed Action on suspended sediment concentrations (SSC) downstream of the dams may be partially mitigated by physical removal of sediment from the reservoirs prior to dam deconstruction. Sediment removal would potentially decrease erosion of the existing reservoir sediment deposits following dam removal and correspondingly decrease the magnitude of suspended fine sediments transported downstream to the lower Klamath River. In support of the EIS/EIR evaluation of dam removal effects on downstream water quality and key fish species, this technical memorandum documents modeling results for a potential sediment removal mitigation measure, including a comparison of model results based on two similar, but not identical, reservoir drawdown scenarios. Details of the Proposed Action and multiple reservoir drawdown scenarios, as well as the approach to mechanical sediment removal from the reservoirs, will be documented elsewhere by the Bureau of Reclamation (USBR) and CDM. Only information relevant to the comparison of the two sediment removal drawdown scenarios for SSC model results and anticipated impacts to focal fish species are summarized below.

dam removal, turbidity, salmon, impacts, dredging
2011Steven T. Lindley, Holly DavisUsing Model Selection and Model Averaging to Predict the Response of Chinook Salmon to Dam Removal. Review Draft., 180102

Removal of four dams from the mainstem Klamath River depends on a cost-benefit analysis that includes expected benefits to fisheries. We predict expected escapement of Chinook salmon to watersheds above Iron Gate Dam using a log-linear modeling approach. Data from 77 populations of Chinook salmon in Washington, Idaho, Oregon, and California are assembled, including average escapement and measures of habitat quantity and quality. Nonmetric multidimensional scaling is used to reveal that adult run timing is related to environmental characteristics of watersheds and show that watersheds above Iron Gate are more similar to spring-run Chinook salmon-bearing watersheds than they are to fall-run Chinook salmon-bearing watersheds. We use model selection and averaging and bootstrap resampling to predict escapement to watersheds above Iron Gate. Models based on spring-run Chinook salmon data only predict escapement of about 3090 spawners per year (90% confidence interval 1420–25,300) to the upper basin, while models based on the complete dataset predict 3660 (2420–5510) spawners per year.

dam removal, anadromy, chinook
2011John G. WilliamsReview of : Using Model Selection and Model Averaging to Predict the Response of Chinook Salmon to Dam Removal and Forecasting the Response of Klamath Basin Chinook Populations to Dam Removal and Restoration of Anadromy Versus No Action, 180102

The Klamath Basin Restoration Agreement (KBRA) calls for the Secretary of the Interior to make a finding by 12 March 2012 whether four dams on the Klamath River should be removed. The two studies under review are intended to inform this decision. In particular, they addess the question whether and by how much removing the dams will increase the production of Klamath Basin Chinook salmon over the coming fifty years; the answer, reached by two different modeling approches, is “Probably, but it is hard to say how much.”Both models give highly uncertain estimates of future production of Klamath Basin Chinook, but that should be expected, and one of the strengths of these models is that they deal explicitly with uncertainty. Both models ignore a good deal of detailed information about the basin, which may make the models seem simplistic and unrealistic, and will upset the people who have developed the information. Both studies fail to take account of two important factors: global warming, and interactions between hatchery and naturally produced salmon. Models are tools of science, not science itself. The two models reviewed here incorporate the best available modeling approaches, but, in my assessment, to meet the standard of “best available science,” the models need to deal with the effects of climate change and interactions with hatchery fish.

dam removal, anadromy, chinook
2011Noble HendrixForecasting the Response of Klamath Basin Chinook Populations to Dam Removal and Restoration of Anadromy Versus No Action, 180102

Two alternative actions are being evaluated in the Klamath Basin: 1) a No Action Alternative (NAA) and 2) removal of four mainstem dams (Iron Gate, Copco I, Copco II, and J.C. Boyle) and initiation of habitat restoration in the Klamath Basin under a Dam Removal Alternative (DRA). The decision process regarding which action to implement requires annual forecasts of abundance with uncertainty under each of the two alternatives from 2012 to 2061. I forecasted escapement for both alternatives by constructing a life-cycle model (Evaluation of Dam Removal and Restoration of Anadromy, EDRRA) composed of: 1) a stock recruitment relationship between spawners and age 3 in the ocean, which is when they are vulnerable to the fishery, and 2) a fishery model that calculates harvest, maturation, and escapement. To develop stage 1 of the model under NAA, I estimated the historical stock recruitment relationship in the Klamath River below Iron Gate Dam in a Bayesian framework. To develop stage 1 of the model under DRA, I used the predictive spawner recruitment relationships in Liermann et al. (2010) to forecast recruitment to age 3 from tributaries to Upper Klamath Lake, which is the site of active reintroduction of anadromy. I also modified the spawner recruit relationship under DRA to include additional spawning capacity between Iron Gate Dam and Keno Dam. In order to facilitate the comparison of the two alternatives, I used paired Monte Carlo simulations to forecast the levels of escapement and harvest under NAA and DRA. Median escapements and harvest were higher in DRA relative to NAA with a high degree of overlap in 95% confidence intervals due to uncertainty in stock-recruitment dynamics. Still, there was a 0.75 probability of higher annual escapement and a 0.7 probability of higher annual harvest by performing DRA relative to NAA, despite uncertainty in the abundance forecasts.

dam removal, anadromoy
2009Nicholas J. Hetrick, T. A. Shaw, P. Zedonis, C. D. ChamberlainCompilation of information to Inform USFWS Principals on the Potential Effects of the Proposed Klamath Basin Restoration Agreement (Draft 11) on Fish and Fish Habitat Conditions in the Klamath Basin, with Emphasis on Fall Chinook Salmon, , , , , , , , 180102

The primary focus of this report is the effects of the proposed Agreements on anadromous fish, and in particular, fall run Chinook salmon. The substantial body of existing information on fall run Chinook below Iron Gate Dam (IGD), as well as several existing peer-reviewed models that address habitats and production of fall run Chinook salmon, provide the basis for considerable in-depth analysis of potential effects in the lower Klamath River. Fewer tools are currently available for examining potential for successful re-occupancy of areas above IGD, but the existing information is sufficient for preliminary analyses. Analytical tools for coho salmon are much more limited, and are virtually non-existent for spring run Chinook, steelhead, and lamprey. As such, this report offers little analysis of the outcomes of the proposed Agreements on those taxa.

fall run chinook, iron gate dam
2012Noble HendrixEvaluation of Long-Term Changes in Klamath Basin Chinook Populations From Dam Removal and Restoration Anadromy Versus No Action, 180102

Decision makers are often faced with having to make a decision without perfect information (Berger 2006, Hilborn and Walters 1992). Decision theory may facilitate this process by providing a framework for evaluating alternative decisions under uncertainty (Berger 2006). By uncertainty, we are most often referring to alternative states of nature (i.e., the set of conditions over which the decision maker has no control). For example, two
states of nature concerning the chance of rain tomorrow are: 1) that it will rain tomorrow or 2) that it will not rain tomorrow. Alternative actions may then be evaluated in light of the uncertain state of nature. Returning
to the rain example, assume that there are two possible actions being considered: 1) bring and umbrella and 2) do not bring an umbrella. One can then evaluate the two actions given the probability of rain obtained, say,
via a weather forecast. Ultimately, the goal of being explicit about the uncertain states of nature and the actions is to make an informed decision. Here the states of nature were binary, but they may also be a much broader
set of conditions that are not under the control of decision makers. In the context of fisheries management these may be biological rates such as the inherent productivity of a species or physical conditions such as
variability in the environment. Here I analyze two alternative actions pertaining to a Chinook salmon (Oncorhynchus tshawytscha) population in the Klamath Basin under uncertain states of nature. This analysis informs the determination by the Secretary of the Interior (Secretarial Determination) regarding the removal of four mainstem dams on the Klamath River (for more information, pleases see klamathrestoration.gov).

dam removal, chinook
1998Ronnie M. PierceKlamath Salmon: Understanding Allocation, , 18010209

This document gives readers a basic understanding of the history and development of Klamath River fall Chinook management and allocation policies. It includes the background of the various fisheries, the legal background and basis of Klamath River Tribal fishing rights, and the background and current principles of Harvest rate Management.

fall chinook, harvest
2016Desiree D. Tullos, Mathias J. Collins, J. Ryan Bellmore, Jennifer A. Bountry, Patrick J. Connolly, Patrick B. Shafroth, and Andrew C. WilcoxSynthesis of Common Management Concerns Associated With Dam Removal180102

Managers make decisions regarding if and how to remove dams in spite of uncertainty surrounding physical and ecological responses, and stakeholders often raise concerns about certain negative effects, regardless of whether these concerns are warranted at a particular site. We used a dam-removal science database supplemented with other information sources to explore seven frequently raised concerns, herein Common Management Concerns (CMCs). We investigate the occurrence of these concerns and the contributing biophysical controls. The CMCs addressed are the following: degree and rate of reservoir sediment erosion, excessive channel incision upstream of reservoirs, downstream sediment aggradation, elevated downstream turbidity, drawdown impacts on local water infrastructure, colonization of reservoir sediments by nonnative plants, and expansion of invasive fish. Biophysical controls emerged for some of the concerns, providing managers with information to assess whether a given concern is likely to occur at a site. To fully assess CMC risk, managers should concurrently evaluate site conditions and identify the ecosystem or human uses that will be negatively affected if the biophysical phenomenon producing the CMC occurs. We show how many CMCs have one or more controls in common, facilitating the identification of multiple risks at a site, and demonstrate why CMC risks should be considered in the context of other factors such as natural watershed variability and disturbance history.

2001Southwest Fisheries Science Center, Santa Cruz LaboratoryStatus Review Update for Coho Salmon (Oncorhynchus kisutch) from the Central California Coast and the California portion of the Southern Oregon/Northern California Coasts Evolutionarily Significant Units, , , , 18010209

Coho salmon (Oncorhynchus kisutch) data in California were reviewed to provide an update of its status. This review was based only on biological information and uses the “best available data” to analyze the current condition of this species. The geographical area covered includes the Central California Coast ESU and the California portion of the Southern Oregon/Northern California Coasts ESU. In previous status reviews, findings were that the Central California Coast ESU was presently in danger of extinction and that the Southern Oregon/Northern California Coasts ESU was likely to become endangered in the foreseeable future.

This status review update agrees with previous BRT conclusions. The Central California Coast ESU is presently in danger of extinction. The condition of coho salmon populations in this ESU is worse than indicated by previous reviews. The California portion of the Southern Oregon/Northern California Coasts ESU is likely to become endangered in the foreseeable future.

coho
2016David MarmorekCan We Restore Ecological Processes and Recover Salmon Populations Below a Dam?18010209

Presentation summarizes lessons learned from the Trinity River Restoration Program, including conceptual models for adaptive management and general recovery strategy.

Trinity River Restoration Program, adaptive management
2013Stillwater Sciences, Jones & Trimiew Design, Atkins, Tetra Tech, Riverbend Sciences, Aquatic Ecosystem Sciences, and NSI/BiohabitatsWater Quality Improvement Techniques for the Upper Klamath Basin: A Technical Workshop and Project Conceptual Designs. Final Report.18010206

The Klamath River Water Quality Workshop was held on September 10-13, 2012 in Sacramento, California, to evaluate large-scale techniques for improving water quality in the Upper Klamath Basin and to inform decision-making on nutrient reduction approaches. The workshop focused on upper basin projects to foster a new, healthier equilibrium condition for basin headwaters, to treat both the symptoms and the causes of elevated phosphorus and nitrogen levels, and, ultimately, to support water quality improvements in downstream reaches of the Klamath River. Workshop participants included over 100 attendees representing roughly 13 federal and state (California, Oregon) agencies, multiple tribes, and several consulting firms, academic institutions, and utilities. Six large-scale pollutant reduction techniques were evaluated at the workshop, including the following: wetland restoration (habitat focus), treatment wetlands (water quality focus), diffuse source (decentralized) treatment wetlands, algal filtration, sediment dredging, sediment sequestration of phosphorus and aeration/oxygenation. This report summarizes information presented at the workshop and, based on feedback from workshop participants and the project Steering Committee, presents conceptual designs for pilot projects to improve water quality in the Upper Klamath Basin.

water quality
2012Stillwater SciencesKlamath River Pollutant Reduction Workshop–Information Packet, , 18010206

Pre-workshop information packet for the Klamath River Pollution Reduction Workshop. Topics covered include: basin overview and potential water treatment technologies (wetland restoration, treatment wetlands, decentralized source treatment systems, and algae/biomass removal, sediment removal, and water column oxidization). Treatment cost estimates are also included.

water quality
2016Conor Shea, Nicholas J. Hetrick, and Nicholas A. Som,Response to Request for Technical Assistance – Sediment Mobilization and Flow History in Klamath River below Iron Gate Dam, , 18010209

The focus of this technical memorandum is to summarize the state of knowledge regarding environmental flow releases from the Iron Gate Dam to achieve specific objectives for channel form and ecological function. Other memorandums in this series will address how achieving these objectives will potentially influence various aspects of the C. Shasta life cycle and population. In this technical memorandum, we first summarize the state of knowledge regarding environmental flows to achieve specific objectives for channel form and ecological function. Then, the memorandum reviews estimates of flows necessary for achieving several channel
substrate movement states in the Klamath River below Iron Gate Dam that were developed by three different research teams. The final section of the memorandum examines the frequency,
magnitude, and duration of sediment mobilization flows for the Klamath River below Iron Gate Dam that have occurred since dam construction.

fish disease, C. shasta, instream flows
2016Nicholas A. Som, Nicholas J. Hetrick, Julie AlexanderResponse to Request for Technical Assistance – Polychaete Distribution and Infections, 18010209

The Arcata Fish and Wildlife Office (AFWO) Fisheries Program is working with its scientific co-investigators to develop a series of four technical memorandums that summarize recent findings of studies that contribute to our current understanding of Ceratanova shasta (syn Ceratomyxa shasta) infections in the Klamath River, in response to requests for technical assistance from the Yurok and Karuk tribes. Each of the topics addressed in the four technical memorandums: 1) geomorphic channel conditions and flow, 2) polychaete distribution and infections, 3) actinospore and myxospore concentrations, and 4) prevalence of C. Shasta infections in juvenile and adult salmonids, are identified in a conceptual model diagram taken from Foott et al. (2011), and as discussed with the requesting tribes. The intent of the technical memorandums is to provide managers with a contemporary understanding of the state of the science with regard to the C. shasta in the Klamath River, and to provide a scientific basis to inform and support resource management decisions. In this technical memorandum, we summarize the state of the science regarding the infection and mortality experience of salmonids exposed to C. shasta in the Klamath River.

fish disease, C. shasta
2016Nicholas A. Som, Nicholas J. HetrickResponse to Request for Technical Assistance – Ceratonova Shasta Waterborne Spore Stages, 18010209

The Arcata Fish and Wildlife Office (AFWO) Fisheries Program is working with its scientific co-investigators to develop a series of four technical memorandums that summarize recent findings of studies that contribute to our current understanding of Ceratanova shasta (syn Ceratomyxa shasta) infections in the Klamath River, in response to requests for technical assistance from the Yurok and Karuk tribes. Each of the topics addressed in the four technical memorandums: 1) geomorphic channel conditions and flow, 2) polychaete distribution and infections, 3) actinospore and myxospore concentrations, and 4) prevalence of C. Shasta infections in juvenile and adult salmonids, are identified in a conceptual model diagram taken from Foott et al. (2011). The intent of the technical memorandums is to provide managers with a contemporary understanding of the state of the science with regard to the C. shasta in the Klamath River, and to provide a scientific basis to inform and support resource management decisions. In this technical memorandum, we summarize the state of the science regarding the waterborne spore stages of the parasite and how they infect the salmonid (via actinospores) and benthic invertebrate (via myxospores) hosts in the Klamath River.

fish disease, C. shasta
2016Nicholas A. Som, Nicholas J. Hetrick, J. Scott Foott, Kimberly TrueResponse to Request for Technical Assistance – Prevalence of C. shasta Infections in Juvenile and Adult Salmonids, 18010209

The Arcata Fish and Wildlife Office (AFWO) Fisheries Program is working with its scientific co-investigators to develop a series of four technical memorandums that summarize recent findings of studies that contribute to our current understanding of Ceratanova shasta (syn Ceratomyxa shasta) infections in the Klamath River, in response to requests for technical assistance from the Yurok and Karuk tribes. Each of the topics addressed in the four technical memorandums: 1) geomorphic channel conditions and flow, 2) polychaete distribution and infections, 3) actinospore and myxospore concentrations, and 4) prevalence of C. Shasta infections in juvenile and adult salmonids, were identified in a conceptual model diagram taken from Foott et al. (2011), and as discussed with the requesting tribes. The intent of the technical memorandums is to provide managers with a contemporary understanding of the state of the science with regard to the C. shasta in the Klamath River, and to provide a scientific basis to inform and support resource management decisions. In this technical memorandum, we summarize the state of the science regarding the infection and mortality experience of salmonids exposed to C. shasta in the Klamath River.

fish disease, C. shasta
2014Clayton CreagerWater Quality Improvement Activities in the Klamath Basin, , , , 180102

This presentation covers the following topics: Klamath Overview, Klamath Fish Health Assessment Team, Klamath River Flow Augmentation Update, Yurok Tribe Environmental Restoration Projects, Salmon River Habitat Restoration, USFS Restoration Projects: Seid and Sugar Creek, Scott and Shasta TMDL Waivers Update, Shasta Watershed Stewardship Pilot Project, Flow Augmentation in the Scott and Shasta Rivers, Scott Valley Groundwater, Upper Klamath Basin Diffuse Source Treatment Wetlands, and BOR Water Quality Improvement Activities.

water quality, monitoring, klamath fish health assessment team
2011Klamath Basin Coordinating CouncilKlamath Basin Restoration Agreement Revised Cost Estimates: Recommendations prepared by the Klamath Cost Review Workgroup and adopted by the Klamath Basin Coordinating Council, , 180102

This document provides an overview of the cost estimates for the Klamath Basin Restoration Agreement. It describes recent updates to the original cost estimates and the basis for those changes. The revised total cost estimate for implementing the KBRA is $799 million for 2012 through 2026. This is an 18 percent reduction from the cost estimates in the 2010 KBRA. The revised estimated costs now average $53 million per year for Federal funding for the KBRA. The revised cost estimates also shifted a number of costs to later years; this reduced the cost estimates in the first seven years by 38 percent.

Secretarial Determination, fall chinook, Shortnose suckers, spawning habitat, spring run chinook
2016John B. Hamilton, Dennis W. Rondorf, William R. Tinniswood, Ryan J. Leary, Tim Mayer, Charleen Gavette, and Lynne A. CasalThe Persistence and Characteristics of Chinook Salmon Migrations to the Upper Klamath River Prior to Exclusion by Dams, 18010206

Historical review substantiates the historical persistence of salmon, their migration characteristics, and the broad population baseline that will be key to future commercial, recreational, and Tribal fisheries in the
Upper Klamath River and beyond.

fall chinoo, spring run chinook, iron gate reservoir
2013U.S. Fish and Wildlife ServiceKlamath River Fish Habitat Assessment Program: Developing Innovative Solutions for Restoring the Klamath River, , , , , , 180102

The Klamath River Fish Habitat Assessment Program, also known as the "Klamath River Flow Study," is providing the data, analytical tools, and models needed to help restore one of the most treasured salmon-producing regions in the United States--the Klamath Basin of Southern Oregon and Northern California. Established by Congress in 2011, the program was initiated to provide a scientific "road map" to help guide the restoration of Klamath River anadromous fishes--salmon, steelhead, sturgeon, and lamprey. This brochure describes major accomplishments of the program and key areas of work.

fall chinook, Shortnose suckers, spawning habitat, spring run chinook, fall run chinook, Secretarial Determination
1991William M. Kier Associates, Klamath Basin Fisheries Task ForceLong Range Plan For The Klamath River Basin Conservation Area Fishery Restoration Program, , , , , , 180102

The U.S. Department of Interior completed a "Klamath River Basin Fisheries Resource Plan" in 1985. It was that plan that Congress had before it when it discussed the proposal that became the Klamath Act. The 1985 plan covered the entire California portion of the Klamath River watershed, including its main tributary, the Trinity River. Recognizing that the Trinity River Fish and Wildlife Management Program was well launched, Congress deleted Trinity restoration from the proposed Klamath Task Force's duties. When it was organized in July, 1987, the Klamath Task Force recognized the need to update the information presented in the 1985 plan and, considering the deletion of the Trinity, to review the earlier plan's restoration approach. This long-range plan is the result of that review. This long-range plan for the Klamath Restoration Program not only updates the 1985 plan, it virtually replaces it by redirecting its principal thrusts.

fall chinook, spawning habitat, iron gate reservoir, spring run chinook, fall run chinook, iron gate hatchery, pacific lamprey
2016Diana Chesney, Morgan KnechtleShasta River Chinook and Coho Salmon Observations in 2015, 180102

A total of 6,745 Fall-run Chinook salmon (Chinook, Oncorhynchus tshawytscha) were estimated to have entered the Shasta River during the 2015 spawning season. An underwater video camera was operated in the flume of the Shasta River Fish Counting Facility (SRFCF) 24 hours a day, seven days a week, from September 1, 2015 until December 21, 2015. The first Chinook was observed on September 8, 2015 and the last Chinook on December 15, 2015. Klamath River Project staff also processed a total of 221 Chinook carcasses during spawning ground surveys, and 8 Chinook carcasses as wash backs against the SRFCF weir (a systematic 1 :1 O sample).

A net total of 77 adult and 31 sub-adult steelhead trout (Oncorhynchus mykiss) were observed passing through the SRFCF during the 2015 season, prior to the removal of the SRFCF on December 21, 2015. An additional net total of four downstream swimming steelhead were detecting using an ARIS sonar unit between January 1, 2016 and February 29, 2016 for a net total of 104 steelhead known to have remained in the Shasta River prior to February 29, 2016. The ARIS unit was in place until May 3, 2016, and footage is currently under review. A technical report will be produced for the entire ARIS period after review and analysis are complete.

fall run chinook, spawning habitat, iron gate hatchery
2015Diana Chesney, Morgan KnechtleShasta River Chinook and Coho Salmon Observations in 2014, 180102

A total of 18,359 fall run Chinook salmon (Chinook, Oncorhynchus tshawytscha) were estimated to have entered the Shasta River during the 2014 spawning season. An underwater video camera was operated in the flume of the Shasta River Fish Counting Facility (SRFCF) twenty four hours a day, seven days a week, from August 29, 2014 until December 10, 2014. The first Chinook was observed on September 6, 2014 and the last Chinook on December 9, 2014. KRP staff also processed a total of 261 Chinook carcasses during spawning ground surveys, 145 Chinook carcasses as wash backs against the SRFCF weir (a systematic 1:10 sample), and 14 Chinook from a trap immediately upstream of the video flume during the season.

fall run chinook, spawning habitat, iron gate hatchery
2014Diana Chesney, Morgan KnechtleShasta River Chinook and Coho Salmon Observations in 2013, 180102

A total of 8,021 fall run Chinook salmon (Chinook, Oncorhynchus tshawytscha) were estimated to have entered the Shasta River during the 2013 spawning season. An underwater video camera was operated in the flume of the Shasta River Fish Counting Facility (SRFCF) twenty four hours a day, seven days a week, from August 28, 2013 until December 9, 2013, when the weir sustained structural damage from ice build-up and was removed. The first Chinook was observed on September 9, 2013 and the last Chinook on December 3, 2013. KRP staff also processed a total of 512 Chinook carcasses during spawning ground surveys (of which 469 were used in fork length histograms), 65 Chinook carcasses as wash backs against the SRFCF weir (a systematic 1:10 sample), and 45 live Chinook in a trap immediately upstream of the video flume during the season.

fall run chinook
2016Morgan Knechtle, Diana Chesney2015 Scott River Salmon Studies Final Report, 180102

The California Department of Fish and Wildlife's (Department), Klamath River Project (KRP) operated a video fish counting facility and conducted cooperative spawning ground surveys (carcass surveys) on the Scott River during the 2015 fall-run Chinook salmon (Chinook, Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) spawning season. The purpose of these surveys is to describe the run characteristics of adult Chinook salmon and coho salmon into the Scott River. Video fish counting operations began on September 30, 2015 and ended on December 9, 2015 due to high river flows. An ARIS sonor camera was installed on December 9, 2015 and operated through December 21, 2015.

The total number of Chinook salmon that entered the Scott River during the 2014 season is estimated to be 2,113 fish. Based on the proportion of male and female Chinook salmon that were sampled during the spawning ground surveys the run was comprised of approximately 573 (27.1%) males and 1,540 (72.9%) females. Based on scale age analysis, adults comprised approximately 99% (2,092 fish) and grilse comprised 1 % (21 fish) of the run. Males ranged in fork length (FL) from 41cm to 105cm and averaged 76.7cm. Females ranged in FL from 39cm to 92cm and averaged 71.9cm. None of the Chinook salmon that returned were estimated to be of hatchery origin.

fall run chinook
2015Morgan Knechtle, Diana Chesney2014 Scott River Salmon Studies Final Report, 180102

The California Department of Fish and Wildlife's (Department) Klamath River Project (KRP) operated a video fish counting facility and conducted cooperative spawning ground surveys (carcass surveys) on the Scott River during the 2014 fall-run Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) spawning season. The purpose of these surveys is to describe the run characteristics of adult Chinook salmon and coho salmon into the Scott River. Video fish counting operations began on September 30, 2014, and ended on December 6, 2014, due to high river flows.

The total number of Chinook salmon that entered the Scott River during the 2014 season is estimated to be 12,471 fish. Based on the proportion of male and female Chinook salmon that were sampled during the spawning ground surveys, the run was comprised of approximately 5,992 (48.0%) males and 6,479 (52.0%) females. Based on scale age analysis, adults comprised approximately 83.55% (10,420 fish) and grilse comprised 16.45% (2,051 fish) of the run. Males ranged in fork length (FL) from 38cm to 105cm and averaged 72.9cm. Females ranged in FL from 44cm to 95cm and averaged 76.2cm. KRP staff estimated that 15 of the Chinook salmon that returned were of hatchery origin.

fall run chinook
2014Morgan Knechtle, Diana Chesney2013 Scott River Salmon Studies Final Report, 180102

The California Department of Fish and Wildlife's (Department), Klamath River Project (KRP) operated a video fish counting facility and conducted cooperative spawning ground surveys (carcass surveys) on the Scott River during the 2013 fall-run Chinook salmon (Oncorhynchus tshawytscha) and coho salmon ( Oncorhynchus kisutch) spawning season. The purpose of these surveys is to describe the run characteristics of adult Chinook salmon and coho salmon into the Scott River. Video fish counting operations began on September 30, 2013, and ended on February 8, 2014, due to high river flows.

The total number of Chinook salmon that entered the Scott River during the 2013 season is estimated to be 4,624 fish. Based on the proportion of male and female Chinook salmon sampled during the spawning ground surveys, the run was comprised of approximately 2,201 (47.6%) males and 2,423 (52.4%) females. Based on scale age analysis, adults comprised approximately 87.3% (4,036 fish) and grilse comprised 12.7% (588 fish) of the run. Males ranged in fork length (FL) from 39 cm to 103 cm and averaged 70.6 cm. Females ranged in FL from 42 cm to 93 cm and averaged 75.0 cm. KRP staff estimated that none of the Chinook salmon that returned were of hatchery origin.

fall run chinook
2016Diana Chesney, Morgan KnechtleKlamath River Project – Recovery of Fall-run Chinook and Coho Salmon at Iron Gate Hatchery October 8, 2015 to December 3, 2015, , 180102

A total of 8,176 fall-run Chinook salmon, (Chinook, Oncorhynchus tshawytscha), entered Iron Gate Hatchery (IGH) during the fall 2015 spawning season from October 8, 2015, through November 25, 2015. Klamath River Project (KRP) staff systematically sampled 1 in every 1 O Chinook, as well as all adipose-clipped Chinook during recovery efforts, for a sample size of 2,343. Scale samples and sex and fork length (FL) data were collected from systematically sampled Chinook. Analysis of the length-frequency distribution for systematically sampled Chinook males indicates that the preliminary cutoff point between grilse and adults occurred at <56 cm FL. Systematically sampled male Chinook ranged in size from 44 to 96 cm FL, and systematically sampled female Chinook ranged from 49 to 89 cm FL. Based on scale age analysis, the Klamath River Technical Team estimated that 2.7% (220) of the run were grilse. Females accounted for 57% (4,643) of the run while males accounted for 43% (3,533). The 2015 Chinook return to IGH contributed roughly 9.8% to the total (Klamath basin) in-river run of 83,846 and 19.0% to the total spawner escapement of 43,125. Based on coded wire tag (CWT) expansion, KRP staff estimated that 82% (6,735) of the Chinook entering IGH during the 2015 season were of hatchery origin.

iron gate hatchery, fall run chinook
2015Diana Chesney, Morgan KnechtleKlamath River Project – Recovery of Fall-run Chinook and Coho Salmon at Iron Gate Hatchery October 7, 2014 to December 19, 2014, , 180102

A total of 25,339 fall-run Chinook salmon (Chinook, Oncorhynchus tshawytscha), entered Iron Gate Hatchery (IGH) during the fall 2014 spawning season from October 7, 2014 through December 19, 2014. Klamath River Project (KRP) staff systematically sampled one in every ten Chinook, as well as all adipose-clipped (AD) Chinook during recovery efforts, for a sample size of 6,491. Scale samples, sex, and fork length (FL) data were collected from systematically sampled Chinook. Analysis of the leng?h­frequency distribution for systematically sampled Chinook males indicates that the preliminary cutoff point between grilse and adults occurred at <60 cm. FL. Systematically sampled male Chinook ranged in size from 48 to 101 cm. FL, and systematically sampled female Chinook ranged from 40 to 91 cm. FL. Based on scale age analysis, the Klamath River Technical Team (KRTT) estimated that 4.1 % (1,039) of the run were grilse. Females accounted for 49% (12,416) of the run while males accounted for 51 % (12,923). The 2014 Chinook return to IGH contributed roughly 13.8% to the total (Klamath basin) in-river run and 17.4% to the total spawner escapement. Based on coded-wire tag (CWT) expansion, KRP staff estimated that 81 % of the Chinook entering IGH during the 2014 season were of hatchery origin.

iron gate hatchery, fall run chinook
2014Diana Chesney, Morgan KnechtleKlamath River Project – Recovery of Fall-run Chinook and Coho Salmon at Iron Gate Hatchery October 8, 2013 to January 21, 2014, , 180102

A total of 14,754 fall-run Chinook salmon, (Chinook, Oncorhynchus tshawytscha, entered Iron Gate Hatchery (IGH) during the fall 2013 spawning season from October 8, 2013 through December 10, 2013. Klamath River Project (KRP) staff systematically sampled 1 in every 10 Chinook, as well as all adipose-clipped (AD) Chinook during recovery efforts, for a sample size of 4,055. Scale samples and sex and fork length data were collected from systematically sampled Chinook. Analysis of the length-frequency distribution for systematically sampled Chinook males indicates that the preliminary cutoff point between grilse and adults occurred at ≤ 59 cm. fork length. Systematically sampled male Chinook ranged in size from 41 to 103 cm. fork length (FL), and systematically sampled female Chinook ranged from 53 to 93 cm. FL. Based on scale age analysis, the Klamath River Technical Team (KRTT) estimated that 8.9% (1,323) of the run were grilse. Females accounted for 48.5% (7,153) of the run while males accounted for 51.5% (7,601). The 2013 Chinook return to IGH contributed roughly 8.2% to the total (Klamath basin) in-river run and 16.7% to the total spawner escapement. Based on coded wire tag expansion, KRP staff estimated that 92% of the Chinook entering IGH during the 2013 season were of hatchery origin.

iron gate hatchery, fall run chinook
2016Morgan Knechtle, Diana ChesneyBogus Creek Salmon Studies 2015 Final Report, , 180102

The California Department of Fish and Wildlife's (CDFW), Klamath River Project (KRP) operated a video fish counting facility and conducted spawning ground surveys ( carcass surveys) on Bogus Creek during the Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) spawning season. The purpose of these surveys is to describe the run characteristics of adult fall-run Chinook salmon and coho salmon into Bogus Creek. Steelhead trout ( Oncorhynchus mykiss) observations are made during the course of sampling for Chinook and coho salmon. Video fish counting operations began on September 8, 2015 and ended on January 15, 2015, at the end of the season. Spawning ground surveys began on October 9, 2015 and were conducted twice a week through December 14, 2015.

spawning habitat, iron gate hatchery
2015Morgan Knechtle, Diana ChesneyBogus Creek Salmon Studies 2014 Final Report, , 180102

The California Department of Fish and Wildlife’s (Department), Klamath River Project (KRP) operated a video fish counting facility and conducted spawning ground surveys (carcass surveys) on Bogus Creek during the Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) spawning season. The purpose of these surveys is to describe the run characteristics of adult fall-run Chinook (Chinook) salmon and coho salmon into Bogus Creek. Steelhead trout (Oncorhynchus mykiss) observations are made during the course of sampling for Chinook and coho salmon. Video fish counting operations began on September 3, 2014 and ended on December 7, 2014 at the end of the season. Spawning ground surveys began on October 10, 2014 and were conducted twice a week through December 5, 2014.

spawning habitat, iron gate hatchery
2014Morgan Knechtle, Diana ChesneyBogus Creek Salmon Studies 2013 Final Report, , 180102

The California Department of Fish and Wildlife’s (Department), Klamath River Project (KRP) operated a video fish counting facility and conducted spawning ground surveys (carcass surveys) on Bogus Creek during the Chinook salmon (Oncorhynchus tshawytscha), coho salmon (Oncorhynchus kisutch) and steelhead trout (Oncorhynchus mykiss) spawning season. The purpose of these surveys is to describe the run characteristics of adult fall-run Chinook (Chinook) salmon, coho salmon and steelhead trout into Bogus Creek. Video fish counting operations began on September 4, 2013 and ended on May 1, 2014 at the end of the season. Spawning ground surveys began on October 14, 2013 and were conducted twice a week through January 24, 2014.

spawning habitat, iron gate hatchery
2016Chantell F. Royer, Andrew P. StubblefieldKlamath Basin Water Quality Monitoring Plan, , , , , 180102

The purpose of the Klamath Basin Water Quality Monitoring Plan is to serve as a foundation for the continued collaboration within the Klamath Basin, by: 1) recommending water quality investigations to answer questions for resource managers, 2) providing for data management, data sharing and data communications to resource managers and other water quality investigators, and 3) provide for consistent sampling methods and quality assurance protocols to assure the comparability of data among the various agencies, watershed groups and tribal governments conducting work within the Klamath Basin.

2016Jackman WilsonContextualizing and Evaluating the Klamath Basin Restoration Agreement, , , 180102

This thesis seeks to contextualize the Klamath Basin Restoration Agreement, and explore the confluence of Western water rights, Indian law, the Endangered Species Act, and the plight of arid farming. It will evaluate the KBRA’s contents and then evaluate the way forward for the agreement to become law. It will also explore whether an agreement like this is the best way of resolving such disputes as opposed to litigation or directly through the legislative process. While the KBRA is not perfect, and its future remains uncertain, it nonetheless provides clarity to a patchwork of conflicting laws, norms and court decisions. Although the KBRA was officially terminated at the beginning of 2016 due to a lack of congressional authorization for the agreement, the Interior Department’s recent decision to allow dam removal has revived the KBRA’s chances of becoming a law. Although it has yet to be enacted and its effects yet to be known, the KBRA represents the best way to provide clarity and stability to the Klamath Basin.

agreement
2012Daniel T. Snyder, John C. Risley, and Jonathan V. Haynes: U.S. Geological SurveyHydrological Information Products for the Off-Project Water Program of the Klamath Basin Restoration Agreement, , , , , , , 180102

The Klamath Basin Restoration Agreement (KBRA) was developed by a diverse group of stakeholders, Federal and State resource management agencies, Tribal representatives, and interest groups to provide a comprehensive solution to ecological and water-supply issues in the Klamath Basin. The Off-Project Water Program (OPWP), one component of the KBRA, has as one of its purposes to permanently provide an additional 30,000 acre-feet of water per year on an average annual basis to Upper Klamath Lake through “voluntary retirement of water rights or water uses or other means as agreed to by the Klamath Tribes, to improve fisheries habitat and also provide for stability of irrigation water deliveries.” The geographic area where the water rights could be retired encompasses approximately 1,900 square miles. The OPWP area is defined as including the Sprague River drainage, the Sycan River drainage downstream of Sycan Marsh, the Wood River drainage, and the Williamson River drainage from Kirk Reef at the southern end of Klamath Marsh downstream to the confluence with the Sprague River. Extensive, broad, flat, poorly drained uplands, valleys, and wetlands characterize much of the study area. Irrigation is almost entirely used for pasture.

2010U.S. Geological SurveyProceedings of the Klamath Basin Science Conference, Medford, Oregon, February 1–5, 2010, , , , , , , , , 180102

This report presents the proceedings of the Klamath Basin Science Conference (February 2010). A primary purpose of the meeting was to inform and update Klamath Basin stakeholders about areas of scientific progress and accomplishment during the last 5 years. Secondary conference objectives focused on the identification of outstanding information needs and science priorities as they relate to whole watershed management, restoration ecology, and possible reintroduction of Pacific salmon associated with the Klamath Basin Restoration Agreement (KBRA). Information presented in plenary, technical, breakout, and poster sessions has been assembled into chapters that reflect the organization, major themes, and content of the conference.

2007Paul McCormick, Sharon G. CampbellEvaluating the Potential for Watershed Restoration to Reduce Nutrient Loading to Upper Klamath Lake, Oregon, , , , , , , , 180102

A literature review of best management practices (BMPs) to reduce nutrient loading was performed to provide information for resource managers in the Klamath Basin, Oregon. Although BMPs have already been implemented in the watershed, some sense of their effectiveness in reducing phosphorus loading and their cost for installation and maintenance is still lacking. This report discusses both causes of nutrient loading and a wide-variety of BMPs used to treat or reduce causal factors. We specifically focused on cattle grazing as the principal land-use and causal factor for nutrient loading in the Klamath Basin above Upper Klamath Lake, Oregon. Several BMP types, including stream corridor fencing, riparian buffer strips and constructed wetlands, seem to have potential for reducing phosphorus loading that may result from cattle grazing. However, no single BMP is likely to be the most effective in all locations or situations.

phosphorus, nitrogen
2014US Department of the InteriorEnvironmental Assessment for Aquatic and Riparian Habitat Enhancement, , , , , , , , ,

The Bureau of Land Management (BLM), Medford District, plays a key role in aquatic and riparian enhancement activities presently underway in the Rogue, Umpqua and Klamath River Systems. Because of the interspersed, checkerboard ownership pattern of the revested Oregon & California Railroad lands, the District works closely with public and private partners to plan aquatic and riparian enhancement projects that benefit resources across ownership boundaries. This Programmatic Aquatic Habitat Enhancement Environmental Assessment (EA) addresses a suite of activities to maintain and restore watershed conditions, establishes the scope and sideboards of the activities, and provides an analysis of the environmental consequences of the typical projects. All proposed activities are consistent with actions identified by NOAA Fisheries / National Marine Fisheries Service (NMFS) and the United States Fish and Wildlife Service (USFWS) in the Programmatic Biological Opinion for Aquatic Restoration Activities in the States of Oregon, Washington and portions of California, Idaho and Nevada (ARBO II). (FWS reference: 01EOFW00-2013-F-0090). The USFWS, NMFS and BLM identified these programmatic activities because they have predictable effects to species and habitat regardless of their location of treatment. Restoration activities that did not have predictable effects (e.g., channel reconstruction projects) or which had uncertainty were not included.

The purpose of the aquatic and riparian enhancement activities proposed in this EA is to maintain or aid recovery of aquatic habitat, riparian habitat, and water quality where a tangible benefit would accrue to resources on public lands.

2016Upper Klamath Special Investment Partnership, Oregon Watershed Enhancement BoardUpper Klamath Special Investment Partnership Accomplishments Summary Report, , , , , 18010206

In January 2012, the Oregon Watershed Enhancement Board authorized the Upper Klamath Special Investment Partnership (UKSIP). The overarching goal of the UKSIP is to contribute to chemical, thermal, and physical aquatic conditions that will benefit fish populations and water quality in the Upper Klamath Basin by reestablishing, improving, and sustaining the ecological and hydrologic connectivity of aquatic ecosystems. This report provides an overview of the progress made by the UKSIP from 2012 to 2015.

suspended sediment, salmon
2016Paul S. Simmons, Somach Simmons & DunnKlamath Basin Restoration Agreement, , , , , , 180102

On December 31, 2015, the Klamath Basin Restoration Agreement (KBRA) terminated because Congress had not enacted legislation necessary for its implementation. Two companion agreements — the Klamath Hydroelectric Settlement Agreement (KHSA) and the Upper Klamath Basin Comprehensive Settlement Agreement (UKBA) — did not by their terms expire, but their planned implementation is interrelated with the now terminated KBRA and they also cannot move forward without the same implementing legislation. This article describes, very generally, the context for the agreements and their major terms, the reasons legislation was necessary, and the state of affairs resulting from the inability to realize federal legislation by the end of 2015.

2013Salmon River Restoration CouncilSalmon River Community Restoration Program Annual Work Plan, ,

Citizen efforts such as the Salmon River Restoration Council are the best vehicle to achieve watershed/fisheries recovery, causing minimal dislocation to existing economic and social activities. Each year the Council has expanded its program to provide remedial actions to prevent and restore the resources of the Salmon River, emphasizing anadromous fish recovery. To date we have brought in over four million dollars worth of improved ecosystem health to the Salmon River. Almost one third of these funds have been an in-kind match provided largely by members of the local community in their volunteer participation in SRRC’s community restoration activities. As is evidenced by the Council’s accomplishments and volunteerism, there is strong community commitment to the protection and restoration of the Salmon River ecosystem, highlighting recovery of the anadromous fisheries. Without the support of the watershed residents and various stakeholders, the recovery and maintenance of the watershed and fisheries is not possible, due to the Salmon River subbasin’s remoteness and access problems. Managing agencies must have the cooperation and support of a well-informed community.

In order to maintain and expand upon our community restoration program, we have created this annual work plan to guide our efforts. Our Program seeks to enlist cooperation and support from the US Forest Service and other federal agencies, the State of California, the Karuk Tribe, resource user groups, the environmental community, recreation users and others to accomplish our goals.

2012Salmon River Restoration CouncilEnvironmental Assessment – Klamath Tributary Coho Rearing Habitat Enhancement Project, , , , 180102

The Bureau of Reclamation (Reclamation) proposes to provide Klamath Basin Restoration Program (KBRP) grant funding to the Salmon River Restoration Council (SRRC) to enhance summer and winter rearing habitats for coho salmon (Oncorhynchus kisutch) at various locations within the Salmon River subbasin, California (see Table 1 and Appendix A.) This Environmental Assessment (EA) has been prepared to examine the potential direct, indirect, and cumulative impacts to the affected environment associated with the proposed action.

This Environmental Assessment (EA) includes discussion of the purpose and need for the proposed project actions, alternatives, environmental consequences of the alternatives, and a listing of agencies and persons consulted (40 CFR 1508.9). The EA was prepared to satisfy the procedural requirements of the National Environmental Policy Act (NEPA) (P.L. 91-190, as amended) and to determine if an Environmental Impact Statement or Finding of No Significant Impact should be prepared.

2011Chantell F. RoyerBuilding a Foundation for Coordinated Water Quality Monitoring in the Klamath River Basin, 180102

The Klamath River basin encompasses 10 million acres in Northern California and Southern Oregon. Salmon decline, coupled with impacts to other beneficial uses, have prompted regulatory agencies to list several rivers as impaired under the Federal Clean Water Act. The 303(d) listing and the subsequent Total Maximum Daily Load (TMDL) development and implementation for improving water quality in the basin have been challenging because coordinated water quality monitoring was lacking within the basin. In response, The North Coast Regional Water Quality Control Board with support from the U. S. Environmental Protection Agency and California Non-point Source Program proposed a contract to facilitate development of a coordinated monitoring plan and a multi-agency water quality monitoring organization within the Klamath basin. The Klamath Watershed Institute, an affiliate of Humboldt State University, was chosen as a neutral party to facilitate the effort. I developed the Klamath Basin Monitoring Plan that identified and mapped the organizations collecting water quality monitoring data, developed a network of monitoring locations for long-term water quality tracking, and identified gaps in current monitoring. Using participatory methods, I facilitated development of a multi-agency organization, the Klamath Basin Monitoring Program, and the collaborative development of a cohesive organizational structure including a shared mission and vision, and gradients of agreement. I identified lessons learned including effective participatory GIS methods and challenges to data sharing. I explored ways of enhancing monitoring efforts using the National Hydrography Dataset – Plus system to provide resource managers with a GIS-based water quality tracking tool and an appropriate scale of resource management.

2003United States Department of Agriculture - Natural Resources Conservation ServiceWork Plan for Adaptive Management Klamath River Basin Oregon and California, , 180102

The Klamath Basin Conservation Districts in Oregon and California requested Natural Resources Conservation Service (NRCS) assistance in developing a strategy to mitigate the impacts of drought on agriculture in the Klamath Basin. The request for planning assistance was triggered by a drought in 2001, impacts of the Endangered Species Act (ESA) listings, and the ensuing elimination of irrigation water during the growing season to over 1,300 farmers.

To mitigate the effects of the drought on agriculture, Conservation Districts throughout the 10-million acre Klamath Basin have focused on four resource concerns: (1) decreasing the amount of water needed for agricultural, (2) increasing water storage, (3) improving water quality, and (4) developing fish and wildlife habitat. To achieve these objectives, the Conservation Districts need timely, quality resource information with which to make decisions, set priorities, and determine the best conservation activities.

2011Sarah E Null, Jay LundFish Habitat Optimization to Prioritize River Restoration Decisions, , , , , , , , 180102

This paper examines and ranks restoration alternatives for improving fish habitat by evaluating tradeoffs between fish production and restoration costs. Optimization modelling is used to maximize out‐migrating coho salmon (Oncorhynchus kisutch) from a natal stream and is applied as a case study in California’s Shasta River. Restoration activities that alter flow and water temperature conditions are the decision variables in the model and include relocating a major diversion, increasing riparian shading, increasing instream flow, restoring a cool‐water spring and removing a dam. A budget constraint limits total restoration expenditures. This approach combines simple fish population modelling with flow and water quality modelling to explore management strategies and aid decision making. Previous fish habitat optimization research typically uses single restoration strategies, usually by altering reservoir releases or modifying outlet structures. Our method enlarges the solution space to more accurately represent extensive and integrated solutions to fish habitat problems. Results indicate that restoration alternatives can be prioritized by fish habitat improvement and restoration cost. For the Shasta River case study, considerable habitat restoration investments were required before fish productivity increased substantially. This exercise illustrates the potential of ecological optimization for highlighting promising restoration approaches and dismissing poor alternatives.

coho
1989A D Olson, J R West,Evaluation of Instream Fish Habitat Restoration Structures in Klamath River Tributaries, 1988/1989, , , 180102

Ten instream fish habitat techniques were evaluated to determine which most effectively restored salmonid spawning and/or rearing conditions. Structure stability was estimated based on how intact each structure remained (by percent) and its age, we then projected useful life for each structure type. Cost in 1989 dollars was used to determine cost per unit habitat area provided. Observed use by spawners was used to estimate total number of redds per structure (over its life). Cost of providing spawning habitat (cost per redd) was calculated by dividing estimated total redds by structure cost.

We rank structures evaluated in this study (from most cost effective to least cost effective) as follows: Digger Logs, Boulder deflectors, Small Boulder Weirs, Boulder Groups with Woody Cover, Free Boulder Weirs, Large Boulder Weirs, Boulder Groups, Boulder/Rootwad Groups, Boulder/Rootwad Deflectors, Small Boulder Weirs, and Cabled Cover Logs.

coho, chinook
2015US Fish and Wildlife ServiceData and Technical Reports Arcata Fish & Wildlife Office, Fisheries Program, , , , , , ,

Arcata Fish and Wildlife Office, Data and Technical Reports, Arcata Fish & Wildlife Office, Fisheries Program.

2016PacifiCorpPacifiCorp Klamath Hydroelectric Project, Including Habitat Conservation Plans, , , , , , 180102

Website includes likes to Habitat Conservation Plans for the Klamath River, including PDFs for the Coho Salmon HCP as well as the HCP for Lost River and Shortnose Suckers. Various technical studies are also available via the website.

coho, suckers
2011US Fish and Wildlife ServiceYreka Fish and Wildlife Office – Ecosystem Habitat Restoration Projects, , , , , 180102

Yreka Fish and Wildlife Office website location for all Ecosystem Habitat Restoration Projects.

salmon
2013US Fish and Wildlife ServiceYreka Fish and Wildlife Office – Planning and Coordination Projects, , , 180102

Yreka Fish and Wildlife Office website location for all Planning and Coordination Projects.

salmon
2013US Fish and Wildlife ServiceYreka Fish and Wildlife Office – Research, Monitoring, and Assessment Projects, , , , 180102

Yreka Fish and Wildlife Office website location for all Research, Monitoring, and Assessment Projects.

salmon, monitoring
2013U.S. Department of the Interior, U.S. Department of Commerce, National Marine Fisheries ServiceKlamath Dam Removal Overview Report for the Secretary of the Interior: An Assessment of Science and Technical Information, , , 180102

This Overview Report and numerous technical reports were developed for the Secretarial Determination by scientists and engineers from Federal agencies working within the Department of the Interior (DOI), the Department of Commerce (DOC), the U.S. Department of Agriculture (USDA), and the U.S. Environmental Protection Agency (USEPA). These agencies worked collaboratively with state agencies from California and Oregon through nine sub-teams of the Technical Management Team (TMT) covering broad topical areas of the Secretarial Determination process. The TMT developed and carried out scientific, engineering, and other technical studies to fill information gaps and address the four questions which inform the Klamath Secretarial Determination identified in the KHSA. These questions are: (1) Would dam removal and KBRA implementation advance salmonid fisheries and other fisheries in the Klamath Basin; (2) What would dam removal entail, what mitigation measures may be needed, and what would these actions cost; (3) What are the major potential risks and uncertainties associated with dam removal; and (4) Would dam removal and implementation of the KBRA be in the public interest?

suspended sediment, iron gate hatchery, salmon
2005Kyna Powers, Pamela Baldwin, Eugene H. Buck, Betsy A. CodyKlamath River Basin Issues and Activities: An Overview, , , , , , , 180102

There have been many studies, Biological Opinions, and operating plans over recent years, all of which have been controversial. The events of 2001 and 2002 prompted renewed efforts to resolve water conflicts in the Klamath Basin. Congress has responded to the controversy in a number of ways, including holding oversight hearings and appropriating funds for activities in the area. This report provides an overview of recent conflict in the Klamath Basin, with an emphasis on activities in the Upper Basin, and summarizes some of the activities taking place to improve water supply reliability and fish survival.

2008National Research CouncilHydrology, Ecology, and Fishes of the Klamath River Basin, , , , 180102

The Klamath River basin is both at the edge and at the center. The basin is a 15,700 square mile watershed at the western rim of North America, where it encompasses a diverse ecosystem, wilderness areas, and irrigated farmlands in southern Oregon and Northern California. The basin is located at the center, however, of the landscape of controversy in American environmental management, and the issues that face Klamath River basin decision makers exemplify in magnified form many of the difficult science and policy challenges that have arisen across the continent. Management of the basin’s hydrologic and ecological resources is complicated because decision makers must sort through a myriad of potential strategies for operating a complex system with interrelated rivers, lakes, marshes, dams, and diversions. The river basin boundaries outline an ecosystem that includes economically valuable water resources and ecologically valuable species, including endangered, threatened, and other fishes, which are dependent on the rivers and lakes for their survival. Alterations to the original hydrologic system began in the late 1800s, accelerated in the early 1900s, and continue today. They include water-control works by private land and water owners, by the large and intricate Klamath Irrigation Project of the U.S. Bureau of Reclamation (USBR), and by several hydroelectric dams operated by a private corporation, PacifiCorp.

spawning habitat, iron gate reservoir,
2004National Research CouncilEndangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery, , , , , , , , , , , 180102

The United States attempts to reduce the rate of extinction within its diverse and valuable biota primarily through the Endangered Species Act (ESA) of 1973. The ESA prohibits or severely limits the intentional or
incidental taking of species that are listed as endangered or threatened. The ESA is ecologically practical in requiring that habitat necessary for each life-history stage (critical habitat) of a species be preserved and, if possible, expanded or enhanced. Among the requirements of the ESA, the prohibition of intentional taking is relatively easy to implement, the prohibition of incidental taking raises many practical difficulties because of its conflict with ordinary human activities, and the requirement for protection of critical habitat can be troublesome in the extreme because it often is in direct conflict with customary and valued uses of natural resources.

The ESA has been applied to the upper Klamath River basin of Oregon and California for protection of the Lost River sucker (Deltistes luxatus) and shortnose sucker (Chasmistes brevirostris) and for the Klamath basin component of a genetically distinct population of coho salmon (Oncorhynchus kisutch) that is designated the southern Oregon/northern California coasts (SONCC) “evolutionarily significant unit” (ESU). The listing of these three fish species has, as required by the ESA, led to an intensive effort on the part of federal agencies and others to identify critical habitat and to propose federal actions that would promote recovery of the species. Analysis of the needs of the species has extended necessarily to private lands and to privately held water rights, given that the fishes range well beyond the boundaries of federal land and water management.

suckers, chinook salmon
2014R. J. Peters, J. J. Duda, G. R. Pess, M. Zimmerman, P. Crain, Z. Hughes, A. Wilson, M.C. Liermann, S.A. Morley, J.R. McMillan, K. Denton, D. Morrill, and K. WarheitGuidelines for Monitoring and Adaptively Managing Restoration of Chinook Salmon (Oncorhynchus tshawytscha) and Steelhead (O. mykiss) on the Elwha River, , , , ,

As of January, 2014, the removal of the Elwha and Glines Canyon dams on the Elwha River, Washington, represents the largest dam decommissioning to date in the United States. Dam removal is the single largest step in meeting the goals of the Elwha River Ecosystem and Fisheries Restoration Act of 1992 (The Elwha Act) — full restoration of the Elwha River ecosystem and its native anadromous fisheries (Section 3(a)). However, there is uncertainty about project outcomes with regards to salmon populations, as well as what the ‘best’ management strategy is to fully restore each salmon stock. This uncertainty is due to the magnitude of the action, the large volumes of sediment expected to be released during dam removal, and the duration of the sediment impact period following dam removal. Our task is further complicated by the depleted state of the native salmonid populations remaining in the Elwha, including four federally listed species. This situation lends itself to a monitoring and adaptive management approach to resource management, which allows for flexibility in decision-making processes in the face of uncertain outcomes.

Chinook Salmon, Steelhead, spawning habitat, suspended sediment
2005John B. Hamilton , Gary L. Curtis , Scott M. Snedaker, David K. WhiteDistribution of Anadromous Fishes in the Upper Klamath River Watershed Prior to Hydropower Dams—A Synthesis of the Historical Evidence, , 18010206

Knowledge of the historical distribution of anadromous fish is important to guide management decisions regarding the Klamath River including ongoing restoration and regional recovery of coho salmon (Oncorhynchus kisutch). Using various sources,we determined the historical distribution of anadromous fish above Iron Gate Dam. Evidence for the largest, most utilized species, Chinook salmon (Oncorhynchus tshawytscha) was available from multiple sources and clearly showed that this species historically migrated upstream into tributaries of Upper Klamath Lake. Available information indicates that the distribution of steelhead (Oncorhynchus mykiss) extended to the Klamath Upper Basin as well. Coho salmon and anadromous lamprey (Lampetra tridentata) likely were distributed upstream at least to the vicinity of Spencer Creek. A population of anadromous sockeye salmon (Oncorhynchus nerka) may have occurred historically above Iron Gate Dam. Green sturgeon (Acipenser medirostris), chum salmon (Oncorhynchus keta), pink salmon (Oncorhynchus gorbuscha), coastal cutthroat trout (Oncorhynchusd arki darkO, and eulachon (Thaleichthysp acificus) were restricted to the Klamath River well below Iron Gate Dam. This synthesis of available sources regarding the historical extent of these species' upstream distribution provides key information necessary to guide management and habitat restoration efforts.

2012Rhea GrahamKlamath River Basin Restoration Nonuse Value Survey Final Report, , , , 180102

This report presents the results from the Klamath survey and summarizes the design and administration of the survey and response rate. Following this description, we provide highlights from the survey responses. Finally, we present the results from the stated preference valuation questions and the aggregate willingness to pay for the river restoration components of the agreements estimated based on the survey responses.

Economic Valuation
2002Yvonne Everett, Merv George, Akimi KingProceedings of the 2001 Klamath Basin Fish & Water Management Symposium, , , , , , , 180102

Major policy issues have emerged in the Klamath River Basin during the past decade. The current or pending restoration, regulatory, statutory and legal issues in the basin include tribal fish and water rights, the Endangered Species Act listings in both Upper Klamath Lake and the mainstem Klamath River, agricultural water rights, and the allocation of water. The magnitude, complexity, and the geographic and political scope of issues and activities in the Klamath Basin call for an integrated approach to policy, funding, data acquisition and resource management. This symposium brought together representatives from the many federal, state and local government agencies, federally-recognized tribes, landowners and citizens, private industry interests, universities, community colleges and non-profit organizations concerned with resource management in the basin. Together we sought to share our current scientific knowledge, restoration experience, regulatory and socio-cultural perspectives, and to make recommendations to promote an integrated basin-wide approach to planning, research, restoration, management and funding efforts aimed at resolving resource issues in the Klamath Basin.

Water Quality, Salmon, Sucker, Habitat Restoration, Amphibians, Riparian Species & Wildlife, Chinook
2014Dr. John DuffieldEconomic Studies of the Value of Fishery Restoration: Benefits of Passage and Reintroduction, , 180102

Economic Studies of the Value of Fishery Restoration: Benefits of Passage and Reintroduction. This presentation provides an overview of Salmon economics since 1950 focusing on Celilo Falls and Kettle Falls. a summary of the current methods of valuing fishery restoration with an overview of 4 contemporary cases: Bristol Bay Wild Salmon Ecosystem (2014), Elwha Dam Removal (1996 study), Dam Removal on the Klamath River (2012) and the Grand Canyon/ Glen Canyon Dam (1994, 2014).

Habitat Restoration, Dam Removal, Salmon
2008Stephen Darby, David SearRiver Restoration Managing the Uncertainty in Restoring Physical Habitat, ,

For many years scientists and river practitioners have recognized the severity and extent to which aquatic ecosystems have been degraded by a variety of human disturbances and activities (Gregory and Park, 1974; Sear and Arnell, 2006). In turn, realization of the widespread nature of the problem has more recently elicited a surge of interest in the possibility of undertaking corrective interventions, such as flow restoration and channel modifications, to restore or rehabilitate lost and/or damaged ecosystem functions (Brookes and Shields, 1996; Wissmar and Bisson, 2003).

Habitat Restoration, Aquatic Habitat, Riparian Species & Wildlife
2016Bruce Aylward, Davíd Pilz, Sarah Kruse, Amy McCoyMeasuring Cost-Effectiveness of Environmental Water Transactions

This report aims to provide context and methodological assistance on the cost-effectiveness of environmental water transactions (EWT) to the various groups that will be involved in this effort. In doing so, we draw on experience with these transactions from the Columbia Basin in the Pacific Northwest, and in states across the western US Specifically, this report aims to assist public funding agencies and project proponents to maximize the cost-effectiveness of investments in projects intended to enhance the quantity of environmental flows. The report provides discussion, guidance and recommendations on cost-effectiveness metrics for environmental water transactions. Detailed instructions for the use of a basic cost-effectiveness metric based on water volumes are laid out, along with an initial testing of the metric to a set of existing transaction data from the Whychus Creek watershed in the Deschutes Basin, Oregon.

water transactions
2016B.C. Chaffin, A.S. Garmestani, H. Gosnell, R.K. CraigInstitutional Networks and Adaptive Water Governance in the Klamath River Basin, USA180102

Polycentric networks of formal organizations and informal stakeholder groups, as opposed to centralized institutional hierarchies, can be critically important for strengthening the capacity of governance systems to adapt to unexpected social and biophysical change. Adaptive governance is one type of environmental governance characterized by the emergence of networks that stimulate adaptive capacity through increases in social-learning, communication, trust, public participation and adaptive management. However, detecting and analyzing adaptive governance networks remains elusive, especially given contexts of highly contested resource governance such as large-scale negotiations over water use. Research methods such as social network analysis (SNA) are often infeasible as they necessitate collecting in-depth and politically sensitive personal data from a near-complete set of actors or organizations in a network. Here we present a method for resolving this problem by describing the results of an institutional SNA aimed at characterizing the changing governance network in the Klamath River Basin, USA during a period of contested negotiations over water. Through this research, we forward a method of institutional SNA useful when an individual or egocentric approach to SNA is problematic for political, logistical or financial reasons. We focus our analysis on publically available data signaling changes in formal relationships (statutory, regulatory, contractual) between organizations and stakeholder groups. We find that employing this type of SNA is useful for describing potential and actual transitions in governance that yield increases in adaptive capacity to respond to social and biophysical surprises such as increasing water scarcity and changes in water distribution.

Water Allocation & Rights
2015Brian C Chaffin, Robin Kundis Craig, Hannah GosnellResilience, Adaptation, and Transformation in the Klamath River Basin Social-Ecological system, 180102

This article uses the four-phase adaptive cycle model that Lance Gunder-son and C.S. Holling described in 2002 to trace the history of the Klamath Basin social-ecological system (“SES”) through periods characterized by vulnerability, resilience, and transformation. We conclude that while Kla-math Basin stakeholders have worked out a compromise settlement that may signify the emergence of a new, more resilient regime of environmental governance, the Basin’s future is uncertain. We identify important thresholds that, if triggered, could move the SES into alternate regimes, and we consider whether formalization of emergent institutions through legislation might influence this trajectory.

Climate Change, Water Allocation & Rights
2014Todd K. BenDor, T. William Lester, Avery Livengood, Adam Davis, Logan YonavjakExploring and Understanding the Restoration Economy

The purpose of this report is to synthesize the evidence and construct a framework for estimating the size of the United States restoration sector. This report is organized as follows: the first section defines restoration, while the second section attempts to define the restoration industry by the factors that drive demand for restoration. The third section reviews previous work to quantify the economic benefits, impacts and contributions of restoration. In the final section, we present our proposed methodology for further research to quantify the size of the restoration industry annually in terms of total economic output and employment.

Restoration, Economy
2010Brian R. Barr, Marni E. Koopman, Cindy Deacon WilliamsPreparing for Climate Change in the Klamath Basin, , , 180102

This report explores how the local communities and natural resources of the Klamath Basin are expected to be affected by climate change and identifies approaches to preparing for such changes.

Climate Change, Monitoring, Aquatic Habitat, Riparian Species & Wildlife
2014Clayton Creager, NCRWQCBWater Quality Improvement Activities in the Klamath Basin, , , , 180102

Presented by Clayton Creager and invited speakers to the North Coast Regional Water Quality Control Board (NCRWQCB).

water quality, presentation, adaptive management, irrigation, salmon, habitat restoration, modelling, land management, steelhead, coho, chinook
N/AKlamath Resource Information SystemKlamath Resource Information System (KRIS), , , , , 180102

The Klamath Resource Information System (KRIS) was initiated in the Klamath and Trinity river basins to track fishery and water quality and restoration trends. Version 1.0 for the Klamath-Trinity was completed in February 1998 and Version 2.0 in April 2001. The Trinity County Resource Conservation District (RCD) is responsible for production of Version 3.0, which was funded through the Trinity River Restoration Program.

Contributions of data, photos and map information from the agencies, Tribes, non-governmental organizations and basin residents were overwhelming. The Cooperators in this project recognize the need to use applied science to protect and restore the health of the Klamath River. They also believe that shared science can be used to build trust with their neighbors. Contact the Trinity County RCD to get CD copies of the database.

database, water quality, amphibians, invertebrates, data, monitoring, streamflow, flow, restoration, vegetation, salmon, sucker, fish
2006Hardy, Thomas B, Addley, Craig REvaluation of Interim Instream Flow Needs in the Klamath River Phase II, , 180102

The purpose of this report is to recommend instream flows on a monthly basis for specific reaches of the main stem Klamath River below Iron Gate Dam by different water year types. These recommendations specify flow regimes that will provide for the long-term protection, enhancement, and recovery of the aquatic resources within the main stem Klamath River in light of the Department of the Interior’s trust responsibility to protect tribal rights and resources as well as other statutory responsibilities, such as the Endangered Species Act. The recommendations are made in consideration of all the anadromous species and life stages on a seasonal basis and do not focus on specific target species or life stages (i.e., coho).

This report details the analytical approach and modeling results from site-specific studies conducted within the main stem Klamath River below Iron Gate Dam downstream to the estuary. Study results are utilized to make revised interim instream flow recommendations necessary to protect the aquatic resources within the main stem Klamath River between Iron Gate and the estuary. This report also makes specific recommendations for future research needs as part of the on-going strategic instream flow studies being undertaken by the U.S. Fish and Wildlife Service and collaborating private, local, state, federal, and tribal
entities.

in-stream flow, habitat restoration, salmon
2016USGSUSGS 11510700 Discharge, Klamath River Below John C. Boyle Powerplant, nr Keno, OR txt18010206

Hourly discharge at USGS gauging station - Oct 2007-Oct2016

discharge, flow
2016USGSUSGS 11510700 Discharge, Klamath River Below John C. Boyle Powerplant, nr Keno, OR csv18010206

Hourly discharge at USGS gauging station - Oct 2007-Oct2016

discharge, flow
2014USGSKlamath Basin Water Rights Place of Use180102

Hydrological Information Products for the Off-Project Water Program of the Klamath Basin Restoration Agreement U.S. Geological Survey Open-File Report 2012-1199 U.S. Department of the Interior By Daniel T. Snyder, John C. Risley, and Jonathan V. Haynes Prepared in cooperation with The Klamath Tribes Access complete report at: http://pubs.usgs.gov/of/2012/1199 Suggested citation: Snyder, D.T., Risley, J.C., and Haynes, J.V., 2012, Hydrological information products for the Off-Project Water Program of the Klamath Basin Restoration Agreement: U.S. Geological Survey Open-File Report 2012, 1199, 17 p., http://pubs.usgs.gov/of/2012/1199 Summary The Klamath Basin Restoration Agreement (KBRA) was developed by a diverse group of stakeholders, Federal and State resource management agencies, Tribal representatives, and interest groups to provide a comprehensive solution to ecological and water-supply issues in the Klamath Basin. The Off-Project Water Program (OPWP), one component of the KBRA, has as one of its purposes to permanently provide an additional 30,000 acre-feet of water per year on an average annual basis to Upper Klamath Lake through voluntary retirement of water rights or water uses or other means as agreed to by the Klamath Tribes, to improve fisheries habitat and also provide for stability of irrigation water deliveries. The geographic area where the water rights could be retired encompasses approximately 1,900 square miles.

water rights
2016J. Ryan Bellmore, Jeffrey J. Duda, Laura S. Craig, Samantha L. Greene, Christian E. Torgersen, Mathias J. Collins and Katherine VittumStatus and Trends of Dam Removal Research in the United States, , NA

Aging infrastructure coupled with growing interest in river restoration has driven a dramatic increase in the practice of dam removal. With this increase, there has been a proliferation of studies that assess the physical and ecological responses of rivers to these removals. As more dams are considered for removal, scientific information from these dam-removal studies will increasingly be called upon to inform decisions about whether, and how best, to bring down dams. This raises a critical question: what is the current state of dam-removal science in the United States? To explore the status, trends, and characteristics of dam-removal research in the U.S., we searched the scientific literature and extracted basic information from studies on dam removal. Our literature review illustrates that although over 1200 dams have been removed in the U.S., fewer than 10% have been scientifically evaluated, and most of these studies were short in duration (<4 years) and had limited (1-2 years) or no pre-removal monitoring. The majority of studies focused on hydrologic and geomorphic responses to removal rather than biological and water-quality responses, and few studies were published on linkages between physical and ecological components. Our review illustrates the need for long-term, multidisciplinary case studies, with robust study designs, in order to anticipate the effects of dam removal and inform future decision making.

dam removal, monitoring, metrics, habitat restoration
2016KHSA PartiesKlamath Agreement in Principle, —— — — — — approach to ensure a sustainable future for the Basin’s tribes, agricultural communities, • Klamath Water Users Association’s notice of potential termination event given • • • • • • • •180102

The four principal parties to the KHSA, the United States through the Departments of the Interior (DOI) and Commerce, the States of California and Oregon, and PacifiCorp have agreed to develop and pursue an administrative path at FERC for facilities removal that preserves the benefits of the KHSA without the need for congressional legislation. To achieve this result, limited amendments to the KHSA are necessary. This Agreement in Principle outlines the process contemplated by the signatories for developing these amendments.

dam removal, license transfer
2016Edward C. Jones, Russell W. Perry, John C. Risley, Nicholas A. Som, and Nicholas J. HetrickConstruction, Calibration, and Validation of the RBM10 Water Temperature Model for the Trinity River, Northern California, 18010211

We present a water temperature model for the Trinity River, a major tributary to the Klamath River. Our model uses publically available simulated meteorological data and observed streamflow data to estimate daily mean water temperature. Previous water-temperature modeling studies of the Trinity River include Zedonis (1997), Deas (1998, 2002), and Watercourse Engineering (2007). We structured our model in River Basin Model-10 (RBM10; Yearsley, 2003, 2009) to be compatible with the RBM10 model for the Klamath River developed by Perry and others (2011). Once calibrated and validated, the Trinity.

water temperature, stream temperature, modelling, augmentation, chinook, salmon
2011Russell W. Perry, John C. Risley, Scott J. Brewer, Edward C. Jones, and Dennis W. RondorfSimulating Water Temperature of the Klamath River Under Dam Removal and Climate Change Scenarios, , 180102

Water temperature simulations were conducted to compare the effect of two management alternatives: the no-action alternative where dams remain in place, and the action alternative where dam removal occurs in 2020 along with habitat restoration. Each management alternative was simulated under historical climate conditions (1961-2010) and six 50-year (2012-2061) climate scenarios. The model selected for the study, River Basin Model-10 (RBM10), was used to simulate water temperatures over a 253-mile reach of the Klamath River located in south-central Oregon and northern California.

dam removal, climate change, water temperature, stream temperature, modelling, simulation