Klamath Basin Integrated Fisheries Restoration and Monitoring Plan - Phase 3 Kick-off Webinar

Clint Alexander, Natascia Tamburello, Marc Porter, Cedar Morton, Darcy Pickard
October 22nd2019

Using existing data from evaluations of habitat restoration, we estimated the average change in coho salmon Oncorhynchus kisutch and steelhead O. mykiss parr and smolt densities for common in-channel
(culvert removal, large wood placement, boulder placement, and constructed logjams) and floodplain
restoration techniques (constructed side channels and reconnected floodplain habitats). We then used these numbers and a Monte Carlo simulation to predict changes in fish numbers in a model watershed for two restoration scenarios: (1) restoration of all accessible habitat within the watershed and (2) restoration of the average amount historically implemented in Puget Sound watersheds (8% of total restorable areas). Mean increases in coho salmon parr or smolt density after restoration ranged from 0.19 to 2.32 parr/m for in-channel techniques and from 0.34 to 1.70 parr/m2 for floodplain techniques. Increases in steelhead parr or smolt density ranged from 0.06 to 0.71 fish/m and from 0.03 to 0.06 fish/m2 for in-channel and floodplain techniques, respectively. Under restoration scenario 1, the predicted mean increase in numbers was 1,459,254 (117%) and 285,302 (140%) for coho salmon parr and smolts and 93,965 (65%) and 28,001 (125%) for steelhead parr and smolts. Under scenario 2, the predicted mean increase in parr and smolts was 59,591 (5%) and 15,022 (7%) for coho salmon and 1,733 (1%) and 1,195 (5%) for steelhead. The percentage of floodplain and in-channel habitat that would have to be restored in the modeled watershed to detect a 25% increase in coho salmon and steelhead smolt production (the minimum level detectable by most monitoring programs) was 20%. However, given the large variability in fish response (changes in density or abundance) to restoration, 100% of the habitat would need to be restored to be 95% certain of achieving a 25% increase in smolt production for either species.

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). It is the USFWS's strategy to improve the status of lampreys by proactively engaging in a concerted conservation effort. This collaborative effort, guided by the development and implementation of the Pacific Lamprey Conservation Initiative (PLCI) initiated in 2004, will facilitate opportunities to address threats, restore habitat, increase our knowledge of Pacific Lamprey, and improve their distribution and abundance in the United States portion of their range.

Juvenile Klamath River Chinook salmon (Oncorhynchus tshawytscha) were assayed from late March to August 2018 by quantitative polymerase chain reaction (QPCR) and histology for myxosporean parasite infection of Ceratonova shasta and Parvicapsula minibicornis. During the first 8 weeks of the season, juvenile Chinook salmon were assayed in real-time for C. shasta. Fish were collected early in the week and processed for necropsy, DNA extraction, and QPCR, in order to provide timely data to fishery managers regarding flow management. Ceratonova shasta prevalence of infection (POI) exceeded the emergency dilution flow criteria of 20% in the Shasta to Scott (K4) reach on April 30th, the 6th week of the monitoring program.
Ceratonova shasta prevalence of infection by QPCR in Chinook salmon collected above the Trinity River confluence during the peak out-migration period (May-July) was 20%, lower than 26% observed in 2017, and 48% in 2016. Parvicapsula minibicornis prevalence of infection in Chinook salmon above the Trinity River confluence for the same time period was 92%, compared to 82% and 89% in 2017 and 2016, respectively.
Among the fish groups tested, naturally produced Chinook salmon had a 11% prevalence of C. shasta infection by QPCR, which was higher than the 5% observed in 2017 but lower than the 27% in 2016. The onset of infection (first detection) in 2018 occurred on April 23 when mean daily river temperature below Iron Gate Dam was 12.5°C. By histology, natural fish sampled from the Shasta to Scott (K4) and Scott to Salmon (K3) reaches from mid-April through the end of May had very low C. shasta POI (0-3%). Ceratonova shasta was not detected in six of the seven sample sets from the two reaches. Additionally, pathology scores were zero for six of seven sample dates, indicating infection levels were well below clinical disease levels in natural Chinook juvenile salmon in the two upper reaches through late spring.

Adult fall Chinook Salmon Oncorhynchus tshawytscha carcasses and redds were surveyed on the mainstem Klamath River, from Iron Gate Dam to Wingate Bar during the 2017 spawning season to estimate annual escapement and characterize the age and sex composition and spawning success of the run. Surveys were conducted over 9 weeks, from October 11 to December 6. Using postmortem mark–recapture methods and a hierarchical latent variables model between Iron Gate Dam and the confluence with the Shasta River, the estimated spawning escapement for this 21.6-km section of the mainstem Klamath River was 4,740 fish. Based on this estimate and age composition data from scale samples, spawning escapement by year class was 1,749 (36.9%) age-2 (jacks and jills), 2,376 (50.1%) age-3, 550 (11.6%) age-4, and 65 (1.4%) age-5 spawners. The presence of jills (age-2 females) was unusually high in 2017 and they accounted for 8.2% of all female carcasses. Jacks (age-2 males) accounted for 53.4% of all male carcasses. An estimated 19.8%
of the fish that spawned in the study area were of hatchery origin. The adult female– male ratio was 1.9:1 and pre-spawn mortality rate of females was 5.5%. Estimated egg deposition by females in the carcass study area was 4.9 million. The redd count in the 125.7-km section of the mainstem river between the Shasta River confluence and Wingate Bar was 478 in 2017. Redd counts over the previous 24-year history of this survey ranged from 243 (in 1993) to 3,456 (in 2014), although the downstream end of these past surveys was the Indian Creek confluence and was thus 11.2 km shorter. Estimated egg deposition in the redd study area was 1.2 million.

This report summarizes data collections and analyses to assess variation in physical habitat characteristics selected by Chinook Salmon smolts in the Trinity River. Spatially, this study focuses on two mainstem Trinity River reaches located downstream of the confluence of the North Fork Trinity River, each several kilometers in length. This project was initiated to inform the extension of the Trinity River Stream Salmonid Simulator (S3) model from the confluence of the North Fork Trinity River to the confluence with the Klamath River.

Several methods for observing and enumerating juvenile Chinook Salmon were explored, with the goal to compliment habitat models developed for Chinook Salmon fry and parr in the upper portion of the Trinity River mainstem. Methods applying various sonar camera technologies were deemed ineffective for the intended needs of the project. To complete the project, direct-observation snorkel counts we chosen as the data collection method.

Time spent conducting field sampling methodology trials and elevated flows causing turbid waters too dark for effective sampling caused delays in implementation of the data collection. Eventually, assessments of habitat use were collected at the desired sites, but during a single week in August. The single week of sampling is generally thought to be too short to capture temporal variation in habitat use. Additionally, the August period of collection is rather late in the period of time when juvenile Chinook Salmon inhabit the Trinity River, and too few wild fish may have been present to accurately reflect the habitat selection of larger juveniles.

This report summarizes results from the 2017 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), near where Interstate 5 crosses the Klamath River (river km 294), and near the Kinsman Creek confluence upstream of the confluence with the Scott River (river km 238). High and variable river flows throughout much of the trapping season prevented the continual operation of traps, contributed to flawed sets at all three trap sites that precluded estimates of abundance, and likely contributed to the overall low catches observed relative to other years. Both frame nets and rotary screw traps were used to sample juvenile salmonids and other fishes. Traps were deployed in late February (Bogus trap site), early March (I-5 trap site), and early June (Kinsman trap site) and were operated until late May (Bogus and I-5 trap sites), or late June (Kinsman trap site). Juvenile salmonids were enumerated daily when traps were operating and subsamples of salmonids were measured for length, weight, and external symptoms of disease. Non-salmonid fishes were also enumerated and subsampled for length measurements. Natural-origin age-0 Chinook Salmon were captured at each of the three trap sites in all weeks that sampling occurred and displayed few external symptoms of disease. Natural-origin juvenile Coho Salmon and steelhead were also observed in relatively low numbers at all three sites during the trapping season.

Water temperature is an important factor in riverine environments, influencing the physiology and life history expression for salmonids and other aquatic organisms. Understanding the thermal regime of a river is a crucial component of successful environmental flow management, especially on rivers with dams and other anthropogenic influences. The U.S. Fish and Wildlife Service began monitoring water temperature in the Klamath basin in 2001 due to growing interest and concern over the effects of elevated water temperatures, particularly on Pacific salmon. This report summarizes the results of 2017 water temperature monitoring for a set of focal locations within the anadromous portion of the Klamath Basin from April 1 to October 31. Temperature criteria for the Trinity River have been recommended by the Trinity River Restoration Program (TRRP) and are based upon the Trinity River Flow Evaluation Study and the Trinity River Mainstem Fishery Restoration: Final Environmental Impact Statement/Environmental Impact Report. On the Klamath River the U.S. Environmental Protection Agency’s (EPA) Pacific Northwest salmonid life history stage temperature criteria are used, as they are the best science-based and peer-reviewed criteria available. In 2017, designated an ‘Extremely Wet’ water year, the Trinity River exceeded temperature criteria for 27 days at the monitoring location above the confluence with the Klamath. The Klamath River exceeded temperature criteria at all sites (range of 24 to 140 days), but only exceeded the long-term mean daily water temperatures at two sites, at Klamath River below Iron Gate Dam and at Klamath River above the mouth. Mean daily water temperatures were < 13.0°C before April 1 at all focal sites and were < 13.0°C after October 31 for 3 of 4 Trinity River focal sites and for 3 of 5 Klamath River focal sites. Most locations saw a decrease in days exceeding temperature criteria from 2016, as well as their respective long-term averages.

David A Hewitt, primarily helps to guide a research and monitoring program for two endangered catostomids in the Upper Klamath Basin of Oregon and California. We use quantitative tools such as capture-recapture to investigate the ecology of the species and factors inhibiting their recovery. Technology for detection of passive integrated transponders (PIT tags) plays a central role.

Biography
Education:
Ph.D. 2009. Marine Science (Fisheries Science/Crustacean Ecology), Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA [Advisor: Dr. Rom Lipcius]

M.S. 2003. Fisheries and Wildlife Sciences (Minor in Statistics), North Carolina State University, Department of Zoology, North Carolina Cooperative Fish and Wildlife Research Unit, Raleigh, NC [Advisor: Dr. Joe Hightower]

B.S. 2000. Fisheries Science, Virginia Tech, Department of Fisheries and Wildlife Sciences, College of Natural Resources, Blacksburg, VA

This document transmits the biological opinion (BiOp) of the U.S. Fish and Wildlife Service (USFWS, Service) based on our review of the proposed operations of the Klamath Project (Project) by the Bureau of Reclamation (Reclamation) in Klamath County in Oregon and Siskiyou and Modoc Counties in California. The federally-listed species (hereafter referred to as listed species) and critical habitats considered in this document are Lost River sucker (Deltistes luxatus, LRS) and shortnose sucker (Chasmistes brevirostris; SNS), which were both listed as endangered in 1988 and have designated critical habitat. There are also listed species that fall under the jurisdiction of the National Marine Fisheries Service (NMFS) that are present in the action area. The effects of the Project on these species was considered in a separate, but coordinated, BiOp prepared by NMFS.

This document was prepared in accordance with section 7 of the Endangered Species Act of 1973, as amended (ESA; 16 U.S.C. § 1531 et seq.). Reclamation’s request for formal consultation was received by the USFWS on December 21, 2018. Reclamation provided an addendum to their December 21 Biological Assessment on February 15, 2019.

This BiOp and the concurrence determinations are based on information provided in Reclamation’s Final Biological Assessment (BA; USBR 2018a), including the addenda and clarifications received on February 15, 2019 and March 22, 2019, and other sources of information. A complete record of this consultation is on file at the USFWS office in Klamath Falls, Oregon.

Despite billions of dollars spent on various river restoration techniques, we still find ourselves debating whether habitat restoration increases fish abundance or concentrates fish. Based on the available literature, I discuss three important questions related specifically to the restoration of salmonid habitat: (1) “Does river restoration increase fish abundance or concentrate fish?”; (2) “Does river restoration increase fish survival or increase abundance?”; and (3) “Does the size or amount of river restoration influence fish response?” First, there is scant evidence to support the contention that river restoration leads to the
concentration of fish at restoration projects. Second, the literature suggests that river restoration may lead to increased survival, increased abundance, or both. Third, recent studies have found little relationship between restoration project length and physical or biological response. The scientific literature does suggest that fish response to restoration varies greatly depending on the watershed template, location, and characteristics of the habitat restoration, and the life history of and limiting factors for a species. Thus, adequately determining whether changes in fish abundance observed in a restored area are due to increased movement, survival, or the amount of restoration will require detailed monitoring of these factors simultaneously.

One of the desired outcomes of dam decommissioning and removal is the recovery of aquatic and riparian ecosystems. To investigate this common objective, we synthesized information from empirical studies and ecological theory into conceptual models that depict key physical and biological links driving ecological responses to removing dams. We define models for three distinct spatial domains: upstream of the former
reservoir, within the reservoir, and downstream of the removed dam. Emerging from these models are response trajectories that clarify potential pathways of ecological transitions in each domain. We illustrate that the responses are controlled by multiple causal pathways and feedback loops among physical and biological components of the ecosystem, creating recovery trajectories that are dynamic and nonlinear. In most cases, short-term effects are typically followed by longer-term responses that bring ecosystems to new and frequently predictable ecological condition, which may or may not be similar to what existed prior to impoundment.

This Biological Assessment (BA) has been prepared pursuant to section 7(a)(2) of the Endangered Species Act (ESA) of 1973, as amended, (16 United States Code [U.S.C.] § 1531 et seq.), to evaluate the potential effects of the continued operation of the Bureau of Reclamation’s (Reclamation) Klamath Project (Project) on species listed as threatened or endangered under the ESA. The Project is located in south-central Oregon and northeastern California and contains approximately 230,000 acres of irrigable land. Reclamation stores, diverts, and conveys waters of the Klamath and Lost Rivers to meet authorized Project purposes and contractual obligations in compliance with state and federal laws and carries out the activities necessary to maintain the Project and ensure its proper long-term functioning and operation.

Federally-listed species that occur within the Action Area and are considered as part of this consultation are the endangered Lost River sucker (Deltistes luxatus), endangered shortnose sucker (Chasmistes brevirostris), threatened Southern Oregon/Northern California Coast (SONCC) coho salmon (Oncorhynchus kisutch), threatened Southern Distinct Population Segment (DPS) of the North American green sturgeon (Acipenser medirostris), endangered Southern Resident DPS killer whale (Orcinus orca), and threatened DPS of Pacific eulachon (Thaleichthys pacificus).

The USDA Forest Service, Six Rivers National Forest (SRNF or forest) has prepared the Six Rivers Aquatic Restoration Project (Aquatic Restoration Project) Draft Environmental Assessment (draft EA), to disclose the environmental analysis of a proposal to accelerate recovery of north coast salmon populations (federally listed threatened coho salmon, steelhead and Chinook salmon), other Forest Service aquatic species and water quality. This assessment was guided by the California Office of Planning and Research 2014 guidance NEPA and CEQA: Integrating Federal and State Environmental Reviews which encourages federal, state and local agencies to coordinate the NEPA and CEQA process so that one environmental document is prepared that meets the requirements for both CEQA and NEPA. The draft EA discloses a range of alternatives and predicted effects of No Action (Alternative 1) compared to the modified Proposed Action (Alternative 2), in compliance with the National Environmental Policy Act (NEPA; 42 USC 4321 et seq.) and the California Environmental Quality Act (CEQA; California Public Resources Code (CPRC) §21000 et seq.).
Alternative 2 represents a programmatic, iterative approach to implementing a suite of phased, forest-wide instream and riparian restoration activities as a step toward fulfilling tribal trust responsibilities, and obligations to local communities, recreationists and commercial fishing industries, SRNF and Klamath National Forest (KNF) land and resource management plans (LRMP or forest plans), and state and federal recovery plan goals (NMFS 2014, CDFG 2004). Alternative 2 aims to rectify and compensate for past natural and human-caused disturbances to aquatic and riparian resources, regardless of the disturbance agent (e.g., floods, landslides, recreational uses, and introduction of invasive plants) by implementing a suite of phased, forest-wide instream and riparian restoration activities.

Role of AFWO Fish & Aquatic Habitat Conservation Program
The U. S. Fish and Wildlife Service’s Fish and Aquatic Habitat Conservation (FAC) Program is responsible for:
1) facilitating the restoration of nationally significant fishery resources,
2) seeking and providing mitigation of fishery resources adversely impacted by federal water development projects,
3) assisting with management of inter-jurisdictional fisheries and fish resources and aquatic habitats,
4) providing technical assistance to native American Tribes, and
5) maintaining a federal leadership role in scientifically-based management of national fishery resources.
Authority and directives supporting Service activities to protect and restore fishery resources and aquatic habitats is described in several acts, including the Fish and Wildlife Act of 1956, Fish and Wildlife Coordination Act, Fish and Wildlife Improvement Act of 1978, Federal Power Act, Anadromous Fish Conservation Act, and Endangered Species Act, and more locally, the Klamath River Basin Fishery Resources Restoration Act, Title 34 of the Central Valley Project Improvement Act, and the Trinity River Basin Fish and Wildlife Restoration Act, among others. The Service has been identified as being DOI’s “principle fact-finding arm and scientific authority on fishery resource matters”, with the role of our FAC Program specified in detail in its national strategic plan titled Strategic Plan for the U.S. Fish and Wildlife Service Fish and Aquatic Conservation Program: FY2016-2020.

Klamath Basin Anadromous Fish and Aquatic Habitat Monitoring and Assessments
The U. S. Fish and Wildlife Service’s Fisheries Program is responsible for: 1) facilitating the restoration of nationally significant fishery resources, 2) seeking and providing mitigation of fishery resources adversely impacted by federal water development projects, 3) providing technical assistance with regard to management of interjurisdictional fisheries and aquatic habitats, and 4) maintaining a federal leadership role in scientifically-based management of national fishery resources. Consistent with this direction, the Service has an established history of working collaboratively on salmon and lamprey issues in the Klamath Basin, with its involvement dating back over 30 years ago with the creation of the Arcata Office to help fulfill the U. S. Government’s trust responsibilities to Native American peoples to restore depleted interjurisdictional salmon resources.

In FY16, the Service’s Arcata Fish and Wildlife Office Fisheries Program, working in collaboration with tribal and agency partners, contributed over 2.4 million dollars in support of monitoring studies, applied research, and to provide technical support needed to better inform management and guide restoration of anadromous fish populations and associated aquatic habitats Northern California. The primary focus of the Program’s activities was within the Klamath Basin and included efforts to support the Trinity River Restoration Program.

Previous methods for constructing univariate habitat suitability criteria (HSC) curves have ranged from professional judgement to kernel-smoothed density functions or combinations thereof. We present a new method of generating HSC curves that applies probability density functions as the mathematical representation of the curves. Compared with previous approaches, benefits of our method include (1) estimation of probability density function parameters directly from raw data, (2) quantitative methods for selecting among several candidate probability density functions, and (3) concise methods for expressing estimation uncertainty in the HSC curves. We demonstrate our method with a thorough example using data collected on the depth of water used by juvenile Chinook salmon (Oncorhynchus tschawytscha) in the Klamath River of northern California and southern Oregon. All R code needed to implement our example is provided in the appendix. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Models that formulate mathematical linkages between fish use and habitat characteristics are applied for many purposes. For riverine fish, these linkages are often cast as resource selection functions with variables including depth and velocity of water and distance to nearest cover. Ecologists are now recognizing the role that detection plays in observing organisms, and failure to account for imperfect detection can lead to spurious inference. Herein, we present a flexible N-mixture model to associate habitat characteristics with the abundance of riverine salmonids that simultaneously estimates detection probability. Our formulation has the added benefits of accounting for demographics variation and can generate probabilistic statements regarding intensity of habitat use. In addition to the conceptual benefits, model application to data from the Trinity River, California, yields interesting results. Detection was estimated to vary among surveyors, but there was little spatial or temporal variation. Additionally, a weaker effect of water depth on resource selection is estimated than that reported by previous studies not accounting for detection probability. N-mixture models show great promise for applications to riverine resource selection.

Precipitation in fall and winter is important to recharge aquifers in Northern California and the Pacific Northwestern United States, causing the baseflow in rivers ascend during the time when Chinook salmon (Oncorhynchus tshawytscha) construct redds. Herein, we evaluate the availability of spawning habitats under a constant streamflow common in regulated rivers against ascending baseflows patterned from free‐flowing rivers. A binomial logistic regression model was applied to predict the suitability of redd locations based on physical characteristics. Next, two‐dimensional hydrodynamic habitat models were developed at two locations representing a broad range of channel forms common in large rivers. Hydrodynamic and habitat models were leveraged together to simulate the quality, amount, and spatial distribution of spawning habitat at a series of individual flow rates, as well as the combined effect of those flow rates
through a spawning season with ascending baseflows. Ascending baseflows increased the abundance of spawning habitat over individual streamflows at a site where the river channel is confined by levee‐like features. However, improvements were greater at an unconfined site that facilitated lateral connectivity and greater expansion of wetted channel area as streamflows increased. Ascending baseflows provided spatial
separation in preferred habitats over a spawning season, which may reduce the risk of superimposition among runs or among species. Ascending baseflows provided a benefit across the range of hydrologic regimes in a 100‐year gauge record ranging from 20% to 122% improvements in habitat area over low streamflows that are currently used to manage for spawning habitat. Although replicating natural flow regimes in managed systems can be impossible or impractical, these results demonstrate that incorporating elements of the natural flow regime like ascending baseflows can benefit the restoration and conservation of riverine species.

Fisheries and water managers often use population models to aid in understanding the effect of alternative water management or restoration actions on anadromous fish populations. We developed the Stream Salmonid Simulator (S3) to help resource managers evaluate the effect of management alternatives on juvenile salmonid populations. S3 is a deterministic stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily time series of discharge, water temperature, and usable habitat area or carrying capacity. The physical characteristics of each habitat unit and the number of fish occupying each unit, in turn, drive survival and growth within each habitat unit and movement of fish among habitat units.

The purpose of this report is to outline the underlying general structure of the S3 model that is common among different applications of the model. We have developed applications of the S3 model for juvenile fall Chinook salmon (Oncorhynchus tshawytscha) in the lower Klamath River. Thus, this report is a companion to current application of the S3 model to the Trinity River (in review). The general S3 model structure provides a biological and physical framework for the salmonid freshwater life cycle. This framework captures important demographics of juvenile salmonids aimed at translating management alternatives into simulated population responses. Although the S3 model is built on this common framework, the model has been constructed to allow much flexibility in application of the model to specific river systems.

A whole lake eutrophication (WLE) model approach for phosphorus and cyanobacterial biomass in Upper Klamath Lake, south-central Oregon, is presented here. The model is a successor to a previous model developed to inform a Total Maximum Daily Load (TMDL) for phosphorus in the lake, but is based on net primary production (NPP), which can be calculated from dissolved oxygen, rather than scaling up a small-scale description of cyanobacterial growth and respiration rates. This phase 3 WLE model is a refinement of the proof-of-concept developed in phase 2, which was the first attempt to use NPP to simulate cyanobacteria in the TMDL model. The calibration of the calculated NPP WLE model was successful, with performance metrics indicating a good fit to calibration data, and the calculated NPP WLE model was able to simulate mid-season bloom decreases, a feature that previous models could not reproduce. In order to use the model to simulate future scenarios based on phosphorus load reduction, a multivariate regression model was created to simulate NPP as a function of the model state variables (phosphorus and chlorophyll a) and measured meteorological and temperature model inputs. The NPP time series was split into a low- and high-frequency component using wavelet analysis, and regression models were fit to the components separately, with moderate success. The regression models for NPP were incorporated in the WLE model, referred to as the “scenario” WLE (SWLE), and the fit statistics for phosphorus during the calibration period were mostly unchanged. The fit statistics for chlorophyll a, however, were degraded. These statistics are still an improvement over prior models, and indicate that the SWLE is appropriate for long-term predictions even though it misses some of the seasonal variations in chlorophyll a.

We describe the methods, structure, and results of the California Freshwater Conservation Success Index (CSI), an assessment tool focused on aquatic species and habitats, the condition of those habitats, and threats those resources will likely face in the future. The CSI uses a common conservation planning approach of subwatershed-scale data summary and scoring, synthesizing and interpreting spatial data for 43 metrics consolidated into 22 indicators. The Aquatic Species Status group of indicators summarizes the findings of a new database of over 400,000 records for 1550 aquatic-dependent species, including all 48 BLM Special Status Species that use freshwater habitats. The Aquatic Habitats Status indicators provide multiple summaries of a multi-source aquatic feature and land cover dataset. A group of Habitat Integrity indicators includes assessment of watershed condition, temperature conditions, habitat connectivity, water quality, water quantity, and land stewardship factors. Future threats are anticipated within indicators related to land conversion, resource extraction, climate change, water quality risk, and introduced species. The combined results map the pattern of relative condition of aquatic species, habitats, condition, and threats across a broad landscape. We provide an example interpretation of how the results of the California Freshwater CSI can be used to identify conservation strategies and discuss important considerations for using the assessment. The results are available as a web map and as a GIS database, allowing users to develop custom queries and configurations of the results for identifying specific opportunities or for evaluating projects.

California’s Central Valley (CCV) Chinook Salmon Oncorhynchus tshawytscha stocks have declined substantially since the mid-1800s, with most listed as threatened or endangered or heavily supplemented by hatcheries. As the largest population of CCV wild spring-run Chinook Salmon, Butte Creek fish are an important source for promoting life history diversity in the CCV Chinook Salmon community. However, little information exists on Butte Creek juvenile mortality during out-migration to the ocean, which is considered a critical phase in the overall population dynamics. We used the Juvenile Salmon Acoustic Telemetry System to track the movement of individual fish, and we used a mark–recapture modeling framework to estimate survival of migrating wild Chinook Salmon smolts from lower Butte Creek to ocean entry at the Golden Gate Bridge. Survival and migration varied significantly among years; in 2015, which was a dry year, Chinook Salmon smolts migrated more slowly throughout their migratory corridor and exhibited lower survival than in a wetter year (2016); among locations, fish migrated faster and experienced higher survival in the lower Sacramento River than in the Sutter Bypass and the Sacramento–San Joaquin River Delta. Our data suggest that higher flow at release and larger fish lengths both resulted in increased survival. Our findings shed light on a critical phase of wild spring-run juvenile Chinook Salmon dynamics and could help to inform future restoration and management projects that would improve the survival and abundance of the CCV spring-run Chinook Salmon populations.

The status of Pacific salmon populations has been of increasing concern for many decades, with many populations now under legal protection. The causes of their declining status are manifold and untangling
them has been difficult due to the complex life histories, which involve migrations among freshwater, estuarine, and marine habitats. Finding solutions to salmon management problems requires understanding
how salmon respond to threats in these different environments. Telemetry provides an attractive approach
to monitoring salmon as they move among these environments, and advances in miniaturization and mass production have made it feasible to monitor salmon throughout their life cycle.

During the summer of 2006, Washington County conducted a fish passage inventory of the culverts acting as road-stream crossings in the Dairy-McKay watershed. The inventory has established a foundation for future fish passage inventories in the County’s other watersheds. Field inspections were conducted on 302 culverts, 164 of which were surveyed and prioritized to identify structures that were barriers to migratory fish species. The remaining culverts were determined non-fish bearing structures. Twenty of the culverts surveyed were deemed high priority barriers and were organized in groupings based on geographic location, stream connectivity, and ease of construction.

Objectives
• Assess fish passage status within Washington County road system in the Dairy- McKay watershed.
• Identify which road-stream crossings act as fish passage barriers (referred to simply as barriers from here on) through field surveys.
• Prioritize and group the barriers by December 2006 to set the groundwork for future replacement.
• Develop a method for incorporating barrier removal into overall project selection, rather than simply incorporating fish passage design into maintenance projects.
• Develop fish passage assessment and prioritization protocol for use throughout the County and by local watershed councils and other transportation entities.
• Foster partnerships to speed replacement of high priority barriers and improve migratory fish access to high quality habitat.

The study area of the Lower Columbia River Ecosystem Restoration Program encompasses the study area of the Lower Columbia Estuary Partnership (Estuary Partnership) and includes all tidally influenced areas of the mainstem and tributaries from Bonneville Dam to the plume. The Columbia River historically supported diverse and abundant populations of fish and wildlife and is thought to have been one of the largest historical producers of Pacific salmonids in the world. Additionally, the lower Columbia River is one of the most important areas in the Pacific Flyway providing migrating, overwintering and/or breeding habitats for shorebirds, waterfowl and neotropical bird species. Anthropogenic changes since the 1860s have significantly reduced the quantity and quality of habitat available to fish and wildlife species. Contributing factors include altered timing, magnitude, duration, frequency, and rate of change in river flows; degraded water quality and increased toxic, chemical contaminants; introduction of invasive exotic species and
altered food web dynamics. Ecosystem-based restoration of the lower Columbia River and estuary has become a regional priority in order to recover its historic productivity and diversity of fish and wildlife.

In 1995 the Estuary Partnership was established by the governors of Washington and Oregon and the US Environmental Protection Agency (USEPA) when USEPA designated the lower Columbia River ‘an estuary of national significance.’ The National Estuary Program (NEP) was established by the US Congress in 1987 amendments to the Clean Water Act to create collaborative, locally driven programs to conserve and restore the nation’s estuaries. The Estuary Partnership is one of the 28 NEPs, and each NEP facilitates and coordinates a collaborative network of partners to implement the actions and meet the goals within its Comprehensive Conservation and Management Plan (Management Plan).

We outlined projected restoration activities for the Upper Klamath River Basin (above Keno), focusing on the geographic scope identified in the Klamath Basin Restoration Agreement (KBRA). Elements of the KBRA budget (Appendix C-2) covered here include row numbers 3, 4, 5, 6, 8, 9, 11, 12, and 90. These activities are intended to improve conditions affecting fish production, survival, and recovery in and above Keno Reservoir and Upper Klamath Lake, with an emphasis on valley-floor rivers and streams. Consequently, areas targeted for these activities are predominately privately-owned, but some publicly managed lands are included. In addition to providing direct benefits to the Upper Klamath Basin, the significant improvements to water quality and nutrient/organic loads expected to result from these actions will benefit the Klamath River for many miles downstream of Keno.
• We did not prioritize restoration activities. Instead, we identified suites of activities by sub-basin that will be fed into the process producing the Phase I Fisheries Restoration Plan under KBRA Section 10.1, which will finalize and prioritize Phase I habitat restoration actions. The Phase I plan will also be informed by an extensive evaluation of past restoration projects that is presently under way, a product of funding by the National Fish and Wildlife Foundation and the Oregon Watershed Enhancement Board.
• Restoration activities and associated costs listed in this document represent the consolidated knowledge
and opinions of many Klamath Basin professionals.

This is an independent expert review of two separate and different approaches for estimating the Chinook salmon production potential of the Klamath River Basin before and after proposed removal of four mainstem dams and implementation of the Klamath Basin Restoration Agreement (KRBA). The information provided in the two modeling endeavors, as well as this and other peer reviews, will be used in a determination to be made by the Secretary of the Interior, in consultation with the Secretary of Commerce,
regarding removal of four hydroelectric dams on the Klamath.

The two reports were reviewed with respect to the stated Terms of Reference. Comments were made on both specific detailed concerns, as well as broader, overarching issues that might influence the appropriateness of respective approaches. Taken together, the reports by Hendrix (2011) and Lindley and Davis (2011) represent significant work contributing to the estimation of the numbers of fish that could
potentially be produced after Klamath River dam removal and implementation of the KRBA. Both approaches described used a variety of innovative and state-of-the-art modeling techniques for their estimates. However, as noted in the detailed review below, there are several major concerns that have the potential to bias the results of both approaches, most likely in a downward direction. The reliance on existing and recent production data per habitat in other watersheds (both Hendrix, and Lindley and Davis)
and within the Klamath (Hendrix) has the potential of underestimating the actual habitat capacity. Prior to further investigations on these issues, however, and assuming other review comments are addressed, I believe the methods presented in the two reports provide sufficiently robust results to serve as preliminary, albeit likely conservative, estimates of the Chinook production benefits to be gained by dam removal and the KRBA program.

The Definite Plan for the Lower Klamath Project prepared by the Klamath River Renewal Corporation (KRRC) implements the Klamath Hydroelectric Settlement Agreement (2010, as amended 2016) (KHSA). The KHSA resolved disputes among numerous parties regarding the relicensing of the Klamath Hydroelectric Project (FERC No. 2082) (KHP). The parties include: U.S. Departments of Interior and Commerce; States of California and Oregon; Humboldt County, California; Yurok and Karuk Tribes; Upper Klamath Water Users Association; conservation and fishing groups; and PacifiCorp, as the licensee for the KHP.

In the KHSA, the parties agreed to a process whereby PacifiCorp and a dam removal entity, now KRRC, would apply to the Federal Energy Regulatory Commission (FERC) to split the KHP into two projects, the KHP and the Lower Klamath Project, and proceed with the actions necessary to achieve dam removal, a free-flowing condition on the Klamath River, and volitional fish passage. The KHP was constructed between 1911 and 1962 and includes eight developments: East Side, West Side, Keno (non-generating), J.C. Boyle, Copco No. 1, Copco No. 2, Fall Creek, and Iron Gate. PacifiCorp operated the KHP under a 50-year license issued by FERC, until the license expired in 2006. PacifiCorp continues to operate the developments under an annual license.

In September 2016, PacifiCorp and KRRC submitted an application to FERC to amend the existing license for the KHP, establish an original license for the Lower Klamath Project consisting of four developments (J.C. Boyle, Copco No. 1, Copco No. 2, and Iron Gate), and transfer the original license for the Lower Klamath Project to the KRRC. At that time, the KRRC also applied to surrender the license for the Lower Klamath Project, including removal of the four developments. Now that the applications have been filed, KRRC is moving forward with the Definite Plan in accordance with Section 7.2 of the KHSA.

Productive capacity can be defined as the “ecological effect” end of a habitat change ® ecological effect
cause–effect pathway. Determining whether and how a habitat manipulation, either inadvertently or deliberately, will affect productive capacity is the key analytical step of habitat management. We describe a process to ensure that this step is conducted in a manner that is rigorous and relevant. The process has four components: (1) determination of management objectives, (2) identification of indicators, (3) analysis of cause–effect pathways linking habitat changes to ecological effects, and (4) determination of strategies to effect desirable habitat change. The core of the process is the third step, in which we propose the use of hypotheses-of-effect, a network of cause–effect linkages leading from habitat change to ecological effects,
to ensure rigorous assessment of possible effects. We illustrate the process using examples of timber management effects on migratory brook trout (Salvelinus fontinalis) and urbanization effects on littoral warm water communities. We argue that this process, in addition to providing a rigorous means of assessing the evidence relevant to a particular issue, also provides an effective tool for examining uncertainty. We advocate the adoption of this process by management agencies as a method for adaptive habitat management.

Unlike previous histories on the subject (the last being in 1976), this one is fully documented by primary references to the original publication or other sources. There are also explanations as to why some of the previous errors occurred.

The detailed history of each introduction, including the primary references, is given. The subsequent history and status of each species in California is given. The attitude of administrators, ichthyologists, fish culturists, fishery biologists, fishermen, and the public toward each introduction is given, and there is a discussion of their value. There is, with respect to California, a review of the present regulations concerning introduced fishes, and a prognostication of the future concerning them.

Approximately 111 full species of freshwater and euryhaline fishes occur in California. (Salton Sea fishes are excluded.) of these, 53 have been introduced from without the state and have been established successfully. Another five subspecies or races have become established. Twelve introduced fishes have uncertain status. Thirty-nine, including one marine fish which was deliberately introduced, have achieved no lasting success. Eight introduced fishes are listed as "hypothetical." Five were scheduled for introduction, but the introductions were never completed. Three species have been listed erroneously in scientific papers as having been introduced. About 26 other species have been formally suggested as introductions. Three species are likely candidates for introduction.

Klamath Basin Integrated Fisheries Restoration and Monitoring Plan (IFRMP)Phase 2 - Real-time Survey Webinar presentation.

Klamath Basin Integrated Fisheries Restoration and Monitoring Plan (IFRMP) Phase 2 (Task 1.2).

In Progress Chapters & Annotated Report OutlineAugust 24, 2018.

The southern distinct population segment (sDPS) of North American green sturgeon (Acipenser medirostris) is an anadromous, long-lived, late maturing species that spawns in the Sacramento River Basin, located in the Central Valley of California. It spends most of its life in the nearshore marine environment and coastal bays and estuaries along the west coast of North America. On April 7, 2006, NMFS listed sDPS green sturgeon as a threatened species under the Endangered Species Act (ESA) (71 FR 17757, April 7, 2006). This determination was based on the fact that the Sacramento River basin contains the only known sDPS spawning population, information suggesting population decline, and habitat loss and degradation in the Sacramento River Basin. Since the listing of the sDPS, a number of habitat restoration actions within the Sacramento River Basin have occurred and spawning has been documented in the Feather and Yuba rivers (Seesholtz et al. 2015; Beccio 2018), but many significant threats have not been addressed. Currently, the majority of sDPS green sturgeon spawning occurs within a single reach of the mainstem Sacramento River, placing the species at increased risk of extinction due to stochastic events.

Recovery Goal, Objective, and Criteria
The goal of this recovery plan is to recover sDPS green sturgeon and consequently remove it from the Federal List of Endangered and Threatened Wildlife. Achieving this goal will have a number of economic, societal, and ecosystem benefits. Delisting of the sDPS may result in opening fisheries that were closed due to direct or incidental sDPS mortality, resulting in economic and recreational benefits. The ESA regulatory burden will also be eased for fisheries, water resource, industrial, and commercial activities. Accomplishing the habitat restoration measures will also result in more functional ecosystems that support other economic activities and contribute to the conservation and recovery of other species.

July 10-11 2018 IFRMP Workshop Summary

Klamath Basin Integrated Fisheries Restoration and Monitoring Plan (IFRMP) Task 1.2 Objectives, Performance Indicators & Monitoring Workshop Pre-Workshop Briefing Package.

Development of an Integrated Fisheries Restoration & Monitoring Plan for the Klamath Basin: Objectives Hierarchy, Key Performance Indicators & Monitoring Framework Workshop.

Presentation Workshop summary.

Objectives of the workshop:

1. Review draft goals & objectives hierarchy and assign candidate key performance indicators to each objective.

2. Working at a basin-wide scale, review major monitoring needs and uncover gaps in our ability to: a) detect cumulative benefits of portfolios of restoration actions, and b) where required, reduce critical uncertainties related to the effectiveness of different classes of restoration actions.

3. Review preliminary ideas for methods to help prioritize restoration actions and monitoring activities.

Overview of Klamath River Dam Removal and Salmon Reintroduction to the Upper Klamath Basin.
A Concurrent Session at the 36th Annual Salmonid Restoration Conference held in Fortuna, California from April 11 – 14, 2018.

The decommissioning and removal of four dams on the Klamath River is on track to occur in 2020. As with recent dam removals, there are a range of expectations and a range of understanding of the process of removing the dams, monitoring the resources, and minimizing direct and indirect impacts on the natural resources and ecological processes in the watershed. This session will provide an update on the implementation of the dam removal and review the schedule of activities as well as plans for monitoring physical and biological aspects of the river. The purpose of this session is to provide a very up-to-date and concise overview of the process being implemented and the proposed schedule of activities.

The Video Recording of the this Session is Located at: https://vimeo.com/album/5137447

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 (Appendix I).

An Update on the Reintroduction Implementation Plan of Anadromous Fishes into the Oregon Portion
of the Upper Klamath Basin was presented by Mark Hereford, Klamath Fisheries Reintroduction Planner, Oregon Department of Fish and Wildlife and Alex Gonyaw, Fisheries Biologist, Klamath Tribes, at the 36th Annual Salmonid Restoration Conference, April 13, 2018.

On a warm September Saturday in 2002, Amy Cordalis stood in a Yurok Tribal Fisheries Department boat on the Klamath River, in response to reports from fishermen that something was amiss on the river. On this stretch of the Yurok Reservation, the river was wide and deep, having wound its way from its headwaters at the Upper Klamath Lake, through arid south-central Oregon to the California coast. Cordalis, then 22, was a summer fish technician intern, whose job was to record the tribe’s daily catch. A college student in Oregon, she’d found a way to spend time with her family and be on the river she’d grown up with — its forested banks and family fishing hole drawing her back year after year.

But that morning, something was wrong. Cordalis watched as adult salmon, one after the other, jumped out of the water, mouths gaping, before plunging back into the river. Her father, Bill Bowers, who was gillnetting farther downriver, looked up to see a raft of salmon corpses floating around the bend. The carcasses piled up on the banks and floated in eddies, as seagulls swept inland to pick at the remains.

Steelhead are an important and valued resource to California's citizens and are an important component of the vast biodiversity of the State. Like many of California's anadromous fish resources, steelhead are declining. Decline of steelhead populations is but one aspect of the present statewide decline in biodiversity, caused by California's burgeoning human population and the ever-increasing demand on natural resources.
This plan focuses on restoration of native and naturally produced (wild) stocks because these stocks have the greatest value for maintaining genetic and biological diversity.

Large rivers constitute small portions of drainage networks but provide important migratory habitats and fisheries for salmon and trout when and where temperatures are sufficiently cold. Management and conservation of coldwater fishes in the current era of rapid climate change require knowing how riverine thermal environments are evolving and the potential for detrimental biological impacts. Robust estimates of warming rates, however, are lacking due to limited long-term temperature monitoring, so we compiled the best available multidecadal records and estimated trends at 391 sites in the 56,500-km river network of the northwestern USA. Warming trends were prevalent during summer and early fall months in recent 20- and 40-year periods (0.18–0.35°C per decade during 1996–2015 and 0.14–0.27°C per decade during 1976–2015), paralleled air temperature trends, and were mediated by discharge trends at regional and local levels. To illustrate the biological consequences of warming later in this century, trend estimates were used
to inform selection of river temperature scenarios and assess changes in thermal exposure of adult Sockeye Salmon Oncorhynchus nerka migrating to four population areas as well as thermal habitat shifts for resident Brown Trout Salmo trutta and Rainbow Trout O. mykiss populations throughout the region. Future warming of 1–3°C would increase Sockeye Salmon exposure by 5–16% (3–143 degree-days) and reduce thermally suitable riverine trout habitats by 8–31% while causing their upstream shift. Effects of those changes on population persistence and fisheries are likely to be context dependent, and strategic habitat restoration or adaptation strategies could ameliorate some biological impairments, but effectiveness will be tempered by the size of rivers, high costs, and pervasiveness of thermal effects.

Although billions of dollars have been spent restoring degraded watersheds worldwide, watershed-scale studies evaluating their effectiveness are rare. To mitigate damage from past logging activities, the floodplain of the upper Chilliwack River watershed (600 km2) was extensively restored from 1996 to 2000 through off-channel habitat restoration. The contribution of restored habitat to watershed-scale production of wild coho (Oncorhynchus kisutch) smolts was estimated through an extensive mark recapture program in 2002. 27%–34% of the production of the estimated 247 200 out-migrating coho smolts could be attributed to the 157 000 m2 of newly created habitat. Area-based habitat models from the literature performed reasonably well in predicting smolt production from restored habitat, providing an acceptable first-order approach for evaluating production benefits of restoration. The costs of smolt production integrated over 30 years ranged from US$0.69–US$10.05 per smolt, falling within the range of hatchery production costs reported elsewhere (typical cost of US$1.00 per smolt) at the most cost-effective restoration sites. This study demonstrates that large-scale habitat restoration can effectively enhance fish production at a watershed scale, at a cost that may be comparable to hatchery smolt production.

Details of the Phase 1 channel rehabilitation activities are given in Appendices C and G and are summarized here. During Phase 1 (2005-2010), 15 rehabilitation projects were completed along the course of the restoration reach (Table 1, Figure 1). Projects were initially focused on removing riparian berms that had encroached on the river following dam closure, lowering floodplains to match the post-ROD flow regime, and creating point bars that would promote a dynamic river. The conceptual model for these activities was that if restraining features were removed, fluvial processes would take over, creating a more dynamic and complex river that, in turn, would offer more productive habitat for fish and wildlife (USFWS AND HVT 1999; USDOI 2000). It was also recognized that the river could not be restored to pre-dam conditions
and that it would have to be scaled down to the post-ROD flow regime (USFWS AND HVT 1999). However, the initial rehabilitation projects produced little immediate dynamic geomorphic response. Consequently, the degree of mechanical intervention and complexity of projects increased over time. The intent of these more intensive projects was, in part, to create immediate habitat and to construct large-scale channel features that would interact with flood flows and drive more rapid channel changes. This change in design strategy was based on lessons learned and, in general terms, is a type of adaptive management, but represents a shift from the foundational notion that a more dynamic river could be created with minimal bank reconstruction (USFWS AND HVT 1999; HVT et al. 2011) .

A goal of the Trinity River Restoration Program is to enhance the production of naturally spawned salmonids by implementing a suite of restoration actions including streamflow management, gravel augmentation and mechanical channel rehabilitation. Short-term monitoring of select channel rehabilitation sites has documented a direct increase in rearing habitat as a result of channel construction activity; however, a companion study failed to detect substantial improvements between 2009 and 2013 at a 64-km restoration reach scale. Here, we analyzed longer term performance of channel rehabilitation sites and the effect of spatiotemporal changes to constructed and natural off channel features to inform the adaptive management process. We assessed the effect of construction, from 2005-2015, at 13 rehabilitation sites surveyed before and after construction. We also developed a sub-sampling protocol to assess trends in the amount of rearing habitat at a total of 22 rehabilitation sites. All data assessed in this report were collected at a Lewiston dam release of 12.7 cms and all analyses were applicable to that streamflow. Rearing habitat increased at 12 of 13 sites after construction. One site, Trinity House Gulch, experienced a 23% decrease in optimal presmolt habitat attributable to fluvial processes that occurred before the first post-construction survey. However, the trend analysis indicated that the level of initial benefit from construction was not sustained over longer time periods at many sites. Ten of 19 sites had less total habitat at the most recent survey than they did at the first survey after construction; 1 of those 10, Hocker Flat, had slightly more optimal habitat. The year of construction does not appear to affect the amount of habitat after construction (n=11 sites) or at the most recent survey (n=19 sites). However, six of seven sites had more habitat at the most recent survey than they did at pre-construction.

The Klamath Project (Project) delivers water for irrigation purposes to over 200,000 acres in southern Oregon and northern California. This 2017 Operations Plan (Plan) describes Project operations that are anticipated to occur during the 2017 spring-summer irrigation season (March 1 to November 15), based upon current and projected hydrologic conditions. The Plan is consistent with Reclamation’s proposed action analyzed in the biological opinions (BiOp) issued jointly by National Oceanic and Atmospheric Administration’s National Marine Fisheries Service (NMFS) and the U.S. Fish and Wildlife Service (USFWS) on May 31, 2013.

This Plan is divided into three sections. The first section describes the estimated water supplies available for Project purposes during the 2017 spring-summer irrigation season. The second section discusses the voluntary water conservation measures that Reclamation and Project water users will employ to manage and conserve limited water resources. The third section address additional operational considerations.

The Klamath Project (Project) delivers water for irrigation purposes to over 200,000 acres in Southern Oregon and Northern California. This 2015 Operations Plan (Plan) describes Project operations that are anticipated to occur during the 2015 spring-summer irrigation season (March 1 to November 15, 2015), based upon current and projected hydrologic conditions. The Plan is consistent with the Reclamation’s proposed action analyzed in the biological opinions issued jointly by National Oceanic and Atmospheric Administration’s National Marine Fisheries Service (NMFS) and the U.S. Fish and Wildlife Service (USFWS) (collectively the Services) on May 31, 2013 Biological Opinion (BiOp). During formal consultation with Services under section 7 of the Endangered Species Act, Reclamation proposed various actions, as further described in the Operation Plan, to mitigate impacts to federally listed species as a result of operation of the Klamath Project. Reclamation must operate as provided in the BiOp in order to remain in compliance with the Endangered Species Act.

This Plan is divided into two sections. The first section describes the estimated water supplies available for Project purposes during the 2015 spring-summer irrigation season. The second section discusses the voluntary drought mitigation measures that the Bureau of Reclamation and Project water users will employ to minimize and manage potential Project water supply shortages.

Management of the commercially important Washington coastal Chinook Salmon Oncorhynchus tshawytscha troll fishery depends on the Chinook Salmon Fishery Regulation Assessment Model (FRAM). The Chinook Salmon FRAM uses historical and contemporary coded wire tag recoveries to estimate abundance and exploitation rates for particular indicator stocks. Those estimates are used to set limits on overall harvest and protect sensitive stocks. Current efforts are underway to implement a newer “base period” (time period on which exploitation rates are based). Our collaboration of science, management, and industry used genetic mixture modeling to provide independent stock composition estimates supporting FRAM recalibration. Genetic modeling suggested that total catch includes a much smaller proportion of a limiting Columbia River stock, a larger fraction of Canadian stocks, and an abundant Oregon coastal stock not previously included in the FRAM. Our results focus attention on particular stocks that will benefit from refinements in the Chinook Salmon FRAM.

1. Adaptive management (AM) was proposed as a rigourous and structured approach to natural resource management that increases learning and reduces uncertainty. It has been adopted as a guiding principle by agencies world-wide, yet its usefulness for guiding management continues to be debated. We propose a new strategy, which we term staged-scale restoration (SSR), to implement AM in a restoration setting while enhancing the scientific rigour, ecological effectiveness and overall efficiency of restoration efforts compared to traditional applications of AM.
2. The SSR approach includes three aspects: (1) experimentally assessing alternative restoration techniques directly on-site in replicated plots using operational-scale equipment, (2) staging, or the successive establishment and evaluation of treated areas over time and (3) scaling, whereby the most successful techniques identified during earlier stages are applied to increasingly larger areas in later stages. A case study illustrates how SSR was used to improve prairie restoration in western Washington, USA.
3. Staged-scale restoration provides several key advantages. It includes a robust experimental design and thus improves the scientific rigour of AM. It is conducted on-site using operational-scale equipment and thus increases the effectiveness of treatments while also providing a platform for refining existing treatments. SSR facilitates collaboration among researchers and managers. By promoting advanced planning and deferring much of the area to be treated to the latter years of a project, SSR reduces the risk of restoration failure. It can be implemented at multiple sites or years, the number and types of treatments to be assessed can be customized and the pace of restoration can be varied.
4. Synthesis and applications. Staged-scale restoration addresses many of the criticisms that have been directed at conventional adaptive management (AM) and provides a scientifically rigourous strategy.

In 1992 the U.S. Congress enacted the Elwha River Ecosystem and Fisheries Restoration Act (Public Law 102-495). The Elwha Act provided funding for the federal acquisition of the Elwha and Glines Canyon dams and required a specific plan to achieve full restoration of the Elwha River ecosystem and fisheries. The U.S. Department of the Interior (DOI et al. 1994) subsequently published the Elwha Report, which found that only through removal of both dams could full restoration be achieved. The need to protect users of the river’s water from adverse impacts of dam removal was also recognized. The Lower Elwha Klallam Tribe (LEKT), Olympic National Park (ONP) of the National Park Service, the Washington Department of Fish
and Wildlife, the U.S. Fish and Wildlife Service (USFWS), and the Northwest Fisheries Science Center (NWFSC) of the National Marine Fisheries Service (NOAA Fisheries Service) worked together to develop the scientific framework for restoring the ecosystem and fisheries on the Elwha River. This technical memorandum presents that framework, known as the Elwha River Fish Restoration Plan (EFRP or the Elwha Plan).

Removal of two hydroelectric dams on the Elwha River, Washington, one of the largest river restoration projects in the United States, represents a unique opportunity to assess the recovery of fish populations and aquatic ecosystems at the watershed scale. The current project implementation does not contain sufficient funding to support comprehensive monitoring of restoration effectiveness. As a result, current monitoring efforts are piecemeal and uncoordinated, creating the possibility that project managers
will not be able to answer fundamental questions concerning salmonid and ecosystem response. We present the initial elements of a monitoring framework designed to assess the effectiveness of dam removal on the recovery of Elwha River salmonids, their aquatic habitats, and the food webs of which they are an integral component. The monitoring framework is linked to the Elwha Fisheries Restoration Plan, which outlines the restoration of native stocks of salmon and relies upon a process of adaptive management. The monitoring framework includes two areas of emphasis—salmonid population recovery and ecosystem response. We provide study design considerations and make recommendations for additional monitoring efforts prior to dam removal. Based on a power analysis, we determined that a minimum of 3–11 years and up to 50 years of monitoring will be required to capture potential ecosystem responses following dam removal. The development of a monitoring plan will be a significant step forward in objectively evaluating the success of Elwha River dam removal.

River restoration is a relatively recent undertaking, with high levels of complexity and uncertainty involved. Many restoration projects have been monitored over the past three decades, however, results have rarely been compared across projects thereby limiting our ability to identify factors that influence restoration outcomes. Programmatic monitoring and evaluation (ProME) that builds on standardized surveys and systematic cross-project comparison allows for collaborative learning, transfer of results across restoration projects and for adaptive management and monitoring. We present a conceptual framework for ProME consisting of four goals and nine principles. First, ProME accounts for complexity, uncertainty, and change in order to contribute to sustainable river management over the long term. Second, ProME promotes collaborative learning and adaptation by standardizing the sampling design for the field surveys at multiple projects and by disseminating findings across stakeholders. Third, ProME verifies to what extent restoration has been achieved, i.e., it must quantify the size and direction of change. Fourth, ProME identifies why the observed effects were present, thereby improving our mechanistic understanding of river functioning. We conclude with potential extensions of the framework (e.g., evaluating cumulative effects of projects within a catchment). Our conceptual framework presents a structured approach toward a more systematic learning and evidence-based action in river restoration, while taking into account the wider picture of environmental change within which river restoration projects will inevitably operate.

Adaptive management (AM) is being employed in a number of programs in the United States to guide
actions to restore aquatic ecosystems because these programs are both expensive and are faced with
significant uncertainties. Many of these uncertainties are associated with prioritizing when, where, and
what kind of actions are needed to meet the objectives of enhancing ecosystem services and recovering
threatened and endangered species. We interviewed nine large-scale aquatic ecosystem restoration
programs across the United States to document the lessons learned from implementing AM. In addition,
we recorded information on ecological drivers (e.g., endangered fish species) for the program, and
inferred how these drivers reflected more generic ecosystem services. Ecosystem services (e.g., genetic
diversity, cultural heritage), albeit not explicit drivers, were either important to the recovery or
enhancement of the drivers, or were additional benefits associated with actions to recover or enhance
the program drivers. Implementing programs using AM lessons learned has apparently helped achieve
better results regarding enhancing ecosystem services and restoring target species populations. The
interviews yielded several recommendations. The science and AM program must be integrated into how
the overall restoration program operates in order to gain understanding and support, and effectively
inform management decision-making. Governance and decision-making varied based on its particular
circumstances. Open communication within and among agency and stakeholder groups and extensive
vetting lead up to decisions. It was important to have an internal agency staff member to implement the
AM plan, and a clear designation of roles and responsibilities, and long-term commitment of other
involved parties.

We implemented and institutionalized an adaptive management (AM) process for the Columbia Estuary Ecosystem Restoration Program, which is a large-scale restoration program focused on improving ecosystem conditions in the 234-km lower Columbia River and estuary. For our purpose, “institutionalized”means the AMprocess and restoration programs are embedded in the work flow of the implementing agencies and affected parties. While plans outlining frameworks, processes, or
approaches to AMof ecosystem restoration programs are commonplace, their establishment for the long term is not. This article presents the basic AMprocess and explains how AMwas implemented and institutionalized. Starting with a common goal, we pursued a well-understood governance and decision-making structure, routine coordination and communication activities, data and information sharing, commitment from partners and upper agency management to the AMprocess, and meaningful cooperation among program managers and partners. The overall approach and steps to implement and institutionalize AM for ecosystem restoration explained here are applicable to situations in which it has been incomplete or, as in our case, the restoration program is just getting started.

Large-scale ecological restoration programs are beginning to supplement isolated projects implemented on rivers and tidal waterways. Nevertheless, the effects of estuary and river restoration often continue to be evaluated at local project scales or by integration in an additive manner. Today, we have sufficient scientific understanding to apply knowledge gained from measuring cumulative impacts of anthropogenic stressors on ecosystems to assessment of ecological restoration. Integration of this knowledge has potential to increase the efficacy of restoration projects that are conducted at several locations but comanaged within the confines of a larger integrative program. We introduce a framework based on a levels-of-evidence approach that facilitates assessment of the cumulative landscape effects of individual restoration actions taken at many different locations. It incorporates data collection at restoration and reference sites, hydrodynamic modeling, geographic information systems, and meta-analyses in a five-stage process: design, data development, analysis, synthesis and evaluation, and application. This framework evolved from the need to evaluate the efficacy of restoration projects that are being implemented in numerous wetlands on the 235 km tidal portion of the Columbia River, USA, which are intended to increase rearing habitat for out-migrating juvenile salmonid fishes.

This study adapts and applies the evidence-based approach for causal inference, a medical standard, to the restoration and sustainable management of large-scale aquatic ecosystems. Despite long-term investments in restoring aquatic ecosystems, it has proven difficult to adequately synthesize and evaluate program outcomes, and no standard method has been adopted. Complex linkages between restorative actions and ecosystem responses at a landscape scale make evaluations problematic and most programs focus on monitoring and analysis. Herein, we demonstrate a new transdisciplinary approach integrating techniques from evidence-based medicine, critical thinking, and cumulative effects assessment. Tiered hypotheses about the effects of landscape-scale restorative actions are identified using an ecosystem conceptual model. The systematic literature review, a health sciences standard since the 1960s, becomes just one of seven lines of evidence assessed collectively, using critical thinking strategies, causal criteria, and cumulative effects categories. As a demonstration, we analyzed data from 166 locations on the Columbia
River and estuary representing 12 indicators of habitat and fish response to floodplain restoration actions intended to benefit culturally and economically important, threatened and endangered salmon. Synthesis of the lines of evidence demonstrated that hydrologic reconnection promoted macrodetritis export, prey availability, and juvenile fish access and feeding. Upon evaluation, the evidence was sufficient to infer cross-boundary,indirect, compounding, and delayed cumulative effects, and suggestive of nonlinear,
landscape-scale, and spatial density effects. Therefore, on the basis of causal inferences regarding food-web functions, we concluded that the restoration program is having a cumulative beneficial effect on juvenile salmon.

Hundreds of millions of dollars have been spent on stream restoration projects to benefit salmonids and other aquatic species across the Pacific Northwest, though only a small percentage of these projects are monitored to evaluate effectiveness and far fewer are tracked for more than 1 or 2 years. The Washington State Salmon Recovery Board and the Oregon Watershed Enhancement Board have spent more than US$500 million on salmonid habitat restoration projects since 1999. We used a multiple before-after–control-impact design to programmatically evaluate the reach-scale physical and biological effectiveness of a subset of restoration actions. A total of 65 projects in six project categories (fish passage, instream habitat, riparian planting, livestock exclusion, floodplain enhancement, and habitat protection) were monitored over an 8-year period. We conducted habitat, fish, and macroinvertebrate surveys to calculate the following indicators: longitudinal pool cross section and depth, riparian shade and cover, large woody debris volumes, fish density, macroinvertebrate indices, and upland vegetation condition class. Results indicate that four categories (instream habitat, livestock exclusions, floodplain enhancements, and riparian plantings) have shown significant improvements in physical habitat after 5 years. Abundance of juvenile Coho Salmon Oncorhynchus kisutch increased significantly at fish passage projects and floodplain enhancement projects, but significant results were not detected for other fish species. Moreover, the
biological response indicators of juvenile salmonid abundance and macroinvertebrate indices showed declines at instream habitat and habitat protection projects, respectively.

This article reviews the key, cross-cutting findings concerning watershed-scale cost-effective placement
of best management practices (BMPs) emerging from the National Institute of Food and Agriculture
Conservation Effects Assessment Project (CEAP) competitive grants watershed studies. The synthesis focuses on two fundamental aspects of the cost-effectiveness problem: (1) how to assess the location- and farmer-specific costs of BMP implementation, and (2) how to decide on which BMPs need to be implemented and where within a given watershed. Major lessons learned are that (1) data availability remains a significant limiting factor in capturing within-watershed BMP cost variability; (2) strong watershed community connections help overcome the cost estimation challenges; (3) detailing cost components facilitates the transferability of estimates to alternative locations and/or economic conditions; and (4) implicit costs vary significantly across space and farmers. Furthermore, CEAP studies showed that (5) evolutionary algorithms provide workable ways to identify costeffective BMP placements; (6) tradeoffs between total conservation costs and watershed-scale cost-effective water quality improvements are commonly large; (7) quality baseline information is essential to solving cost-effectiveness problem; and (8) systemic and modeling uncertainties alter cost-effective BMP placements considerably.

Conservation and recovery plans for endangered species around the world, including the US
Endangered Species Act (ESA), rely on habitat assessments for data, conclusions and planning of short and
long-term management strategies. In the Pacific Northwest of the United States, hundreds of millions of
dollars ($US) per year are spent on thousands of restoration projects across the extent of ESA-listed Pacific
salmon—often without clearly connecting restoration actions to ecosystem and population needs.
Numerous decentralized administrative units select and fund projects based on agency/organization needs
or availability of funds with little or no centralized planning nor post-project monitoring. The need
therefore arises for metrics to identify whether ecosystem and species level restoration needs are being met by the assemblage of implemented projects. We reviewed habitat assessments and recovery plans to
identify ecological needs and statistically compared these to the distribution of co-located restoration
projects. We deployed two metrics at scales ranging from the sub-watershed to ESA listing units; one
describes the unit scale match/mismatch between projects and ecological concerns, the other correlates
ecological need with need treated by projects across units. Populations with more identified ecological
concerns contained more restoration effort, but the frequency of ecological concerns in recovery plans did
not correlate with their frequency as restoration targets. Instead, restoration projects were strongly biased
towards less expensive types. Many ESA-listed salmon populations (78%) had a good match between need
and action noted in their recovery plan, but fewer (31%) matched at the smaller sub-watershed scale.
Further, a majority of sub-watersheds contained a suite of projects that matched ecological concerns no
better, and often worse, than a random pick of all project types.

Biogenic features such as beaver dams, large wood, and live vegetation are essential to the maintenance of complex stream ecosystems, but these features are largely absent from models of how streams change over time. Many streams have incised because of changing climate or land-use practices. Because incised streams provide limited benefits to biota, they are a common focus of restoration efforts. Contemporary models of long-term change in streams are focused primarily on physical characteristics, and most restoration efforts are also focused on manipulating physical rather than ecological processes. We present an alternative view, that stream restoration is an ecosystem process, and suggest that the recovery of incised streams is largely dependent on the interaction of biogenic structures with physical fluvial processes. In particular, we propose that live vegetation and beaver dams or beaver dam analogues can substantially accelerate the recovery of incised streams and can help create and maintain complex fluvial ecosystems.

Ecological research demonstrates that the most diverse, ecologically valuable river habitats are those associated with dynamically migrating, flooding river channels. Thus, allowing the river channel to “heal itself” through setting aside a channel migration zone, or erodible corridor, is the most sustainable strategy for ecological restoration. The width and extent of channel can be set from historical channel migration and model predictions of future migration. However, the approach is not universally applicable because not all rivers have sufficient stream power and sediment load to reestablish channel complexity on a time scale of decades to years, and many are restricted by levees and infrastructure on floodplains that preclude allowing the river a wide corridor. A bivariate plot of stream power/sediment load (y axis) and degree of encroachment (urban, agricultural, etc.) (x axis) is proposed as a framework for evaluating the suitability of various restoration approaches. Erodible corridors are most appropriate where both the potential for channel dynamics and available space are high. In highly modified, urban channels, runoff patterns are altered, and bottomlands are usually encroached by development, making a wide corridor infeasible. There, restoration projects can still feature deliberately installed components such as riparian trees and trails with the social benefits of public education and providing recreation to underserved families. Intermediate approaches include partial restoration of flow and sediment load below dams and “anticipatory management”: sites of bank erosion are anticipated, and infrastructure is set back in advance of floods, to prevent “emergency” dumping of concrete rubble down eroding banks during high water.

For decades, Channel Evolution Models have provided useful templates for understanding morphological responses to disturbance associated with lowering base level, channelization or alterations to the flow and/or sediment regimes. In this paper, two well-established Channel Evolution Models are revisited and updated in light of recent research and practical experience. The proposed Stream Evolution Model
includes a precursor stage, which recognizes that streams may naturally be multi-threaded prior to disturbance, and represents stream evolution as a cyclical, rather than linear, phenomenon, recognizing an evolutionary cycle within which streams advance through the common sequence, skip some stages entirely, recover to a previous stage or even repeat parts of the evolutionary cycle.

The hydrologic, hydraulic, morphological and vegetative attributes of the stream during each evolutionary stage provide varying ranges and qualities of habitat and ecosystem benefits. The authors’ personal experience was combined with information gleaned from recent literature to construct a fluvial habitat scoring scheme that distinguishes the relative, and substantial differences in, ecological values of different evolutionary stages. Consideration of the links between stream evolution and ecosystem services leads to improved understanding of the ecological status of contemporary, managed rivers compared with their historical, unmanaged counterparts. The potential utility of the Stream Evolution Model, with its interpretation of habitat and ecosystem benefits includes improved river management decision making with respect to future capital investment not only in aquatic, riparian and floodplain conservation and restoration but also in interventions intended to promote species recovery.

Process-based restoration aims to reestablish normative rates and magnitudes of physical, chemical, and biological processes that sustain river and floodplain ecosystems. Ecosystem conditions at any site are governed by hierarchical regional, watershed, and reach-scale processes controlling hydrologic and sediment regimes; floodplain and aquatic habitat dynamics; and riparian and aquatic biota. We outline and illustrate four process-based principles that ensure river restoration will be guided toward sustainable actions: (1) restoration actions should address the root causes of degradation, (2) actions must be consistent with the physical and biological potential of the site, (3) actions should be at a scale commensurate with environmental problems, and (4) actions should have clearly articulated expected outcomes for ecosystem dynamics. Applying these principles will help avoid common pitfalls in river restoration, such as creating habitat types that are outside of a site’s natural potential, attempting to build static habitats in dynamic environments, or constructing habitat features that are ultimately overwhelmed by unconsidered system drivers.

Gravel-bedded streams are thought to have a characteristic meandering form bordered by a selfformed,
fine-grained floodplain. This ideal guides a multibillion-dollar stream restoration industry. We have mapped and dated many of the deposits along mid-Atlantic streams that formed the basis for this widely accepted model. These data, as well as historical maps and records, show instead that before European settlement, the streams were small anabranching channels within extensive vegetated wetlands that accumulated little sediment but stored substantial organic carbon. Subsequently, 1 to 5 meters of slackwater sedimentation, behind tens of thousands of 17th- to 19th-century milldams, buried the presettlement wetlands with fine sediment. These findings show that most floodplains along mid-Atlantic streams are actually fill terraces, and historically incised channels are not natural archetypes for meandering streams.

1.Increasingly, river managers are turning from hard engineering solutions to ecologically based restoration activities in order to improve degraded waterways. River restoration projects aim to maintain or increase ecosystem goods and services while protecting downstream and coastal ecosystems. There is growing interest in applying river restoration techniques to solve environmental problems, yet little agreement exists on what constitutes a successful river restoration effort.
2. We propose five criteria for measuring success, with emphasis on an ecological perspective. First, the design of an ecological river restoration project should be based on a specified guiding image of a more dynamic, healthy river that could exist at the site. Secondly, the river’s ecological condition must be measurably improved. Thirdly, the river system must be more self-sustaining and resilient to external perturbations so that only minimal follow-up maintenance is needed. Fourthly, during the construction phase, no lasting harm should be inflicted on the ecosystem. Fifthly, both pre- and postassessment must be completed and data made publicly available.
3. Determining if these five criteria have been met for a particular project requires development of an assessment protocol. We suggest standards of evaluation for each of the five criteria and provide examples of suitable indicators.
4. Synthesis and applications. Billions of dollars are currently spent restoring streams and rivers, yet to date there are no agreed upon standards for what constitutes ecologically beneficial stream and river restoration. We propose five criteria that must be met for a river restoration project to be considered ecologically successful. It is critical that the broad restoration community, including funding agencies, practitioners and citizen restoration groups, adopt criteria for defining and assessing ecological success in restoration. Standards are needed because progress in the science and practice.

The results of this study could be useful in helping to prioritize which drained wetlands may provide the greatest benefits with regard to reducing nutrient loads to the lake if restoration or landuse modifications are instituted. Recent acquisition and planned restoration of drained wetland areas at the Wood River and Williamson River North properties may produce significant reduction in the quantity of nutrients released by the decomposition of peat soils of these areas. If the water table rises to pre-drainage levels, the peats soils may become inundated most of the year, resulting in the continued long-term storage of nutrients within the peat soils by reducing aerobic decomposition. The maximum benefit, in terms of decreasing potential nutrient loss due to peat decomposition, could be the reduction of total nitrogen and total phosphorus loss to about onehalf that of the 1994–95 annual loss estimated for all the drained wetlands sampled for this study.

Upper Klamath Lake is a large (140 square-mile), shallow (mean depth about 8 ft) lake in south-central Oregon that the historical record indicates has been eutrophic since its discovery by non-Native Americans. In recent decades, however, the lake has had annual occurrences of near-monoculture blooms of the blue-green alga Aphanizomenon flos-aquae. In 1988 two sucker species endemic to the lake, the Lost River sucker (Deltistes luxatus) and the shortnose sucker (Chasmistes brevirostris), were listed as endangered by the U.S. Fish and Wildlife Service, and it has been proposed that the poor water quality conditions associated with extremely long and productive blooms are contributing to the decline of those species.

We calibrated the watershed model SPARROW (Spatially Referenced Regressions on Watershed attributes) to give estimates of suspended-sediment loads for western Oregon and parts of northwestern California. Estimates of suspended-sediment loads were derived from a nonlinear least squares regression that related explanatory variables representing landscape and transport conditions to measured suspended-sediment loads at 68 measurement stations. The model gives estimates of model coefficients and their uncertainty within a spatial framework defined by the National Hydrography Dataset Plus hydrologic network. The resulting model explained 64 percent of the variability in suspended-sediment yield and had a root mean squared error value of 0.737. The predictor variables selected for the final model were (1) generalized lithologic province, (2) mean annual precipitation, and (3) burned area (by recent wildfire). Other landscape characteristics also were considered, but they were not significant predictors of sediment transport, were strongly correlated with another predictor variable, or were not as significant as the predictors selected for the final model.

Knowledge of the regionally important patterns and factors in suspended-sediment sources and transport could support broad-scale, water-quality management objectives and priorities. Because of biases and limitations of this model, however, these results are most applicable for general comparisons and for broad areas such as large watersheds. For example, despite having similar area, precipitation, and land-use, the Umpqua River Basin generates 68 percent more suspended sediment than the Rogue River Basin, chiefly because of the large area of Coast Range sedimentary province in the Umpqua River Basin.

A series of 30-day biochemical oxygen demand (BOD) experiments were conducted on water column
samples from a reach of the upper Klamath River that experiences hypoxia and anoxia in summer. Samples
were incubated with added nitrification inhibitor to measure carbonaceous BOD (CBOD), untreated to
measure total BOD, which included demand from nitrogenous BOD (NBOD), and coarse-filtered to examine
the effect of removing large particulate matter. All BOD data were fit well with a two-group model, so named because it considered contributions from both labile and refractory pools of carbon: BODt=a1(1−e−a0t)+ a2t. Site-average labile first-order decay rates a0 ranged from 0.15 to 0.22/day for CBOD and 0.11 to 0.29/day for BOD. Site-average values of refractory zero-order decay rates a2 ranged from 0.13 to 0.25 mg/L/day for CBOD and 0.01 to 0.45 mg/L/day for BOD; the zero-order CBOD decay rate increased from early- to midsummer. Values of ultimate CBOD for the labile component a1 ranged from 5.5 to 28.8 mg/L for CBOD, and 7.6 to 30.8 mg/L for BOD. Two upstream sites had higher CBOD compared to those downstream. Maximum measured total BOD5 and BOD30 during the study were 26.5 and 55.4 mg/L; minimums were 4.2 and 13.6 mg/L. For most samples, the oxygen demand from the three components considered here were: labile CBOD>NBOD>refractory CBOD, though the relative importance of refractory CBOD to oxygen demand increased over time. Coarse-filtering reduced CBOD for samples with high particulate carbon and high biovolumes of Aphanizomenon flos-aquae. There was a strong positive correlation between BOD, CBOD, and the labile component of CBOD to particulate C and N, with weaker positive correlation to field pH, field dissolved oxygen, and total N. The refractory component of CBOD was not correlated to particulate matter, instead showing weak but statistically significant correlation to dissolved organic carbon, UV absorbance at 254 nm, and total N.

A hydrodynamic, water temperature, and water-quality model was constructed for a 20-mile reach of the Klamath River downstream of Upper Klamath Lake, from Link River to Keno Dam, for calendar years 2006–09. The two-dimensional, laterally averaged model CE-QUAL-W2 was used to simulate water velocity, ice cover, water temperature, specific conductance, dissolved and suspended solids, dissolved oxygen, total nitrogen, ammonia, nitrate, total phosphorus, orthophosphate, dissolved and particulate organic matter, and three algal groups. The Link–Keno model successfully simulated the most important spatial and temporal patterns in the measured data for this 4-year time period. The model calibration process provided critical insights into water-quality processes and the nature of those inputs and processes that drive water quality in this reach. The model was used not only to reproduce and better understand water-quality conditions that occurred in 2006–09, but also to test several load-reduction scenarios that have implications for future water-resources management in the river basin.

The model construction and calibration process provided results concerning water quality and transport in the Link–Keno reach of the Klamath River, ranging from interesting circulation patterns in the Lake Ewauna area to the nature and importance of organic matter and algae.

We tested the hypothesis that there would be measurable losses of phosphorus (P) from surficial sediments of Upper Klamath Lake (UKL), Oregon, if sediments were a source of P during an algal bloom.
We compared concentrations of total and forms of P at various depths in cores collected before and after
the onset of a large Aphanizomenon flos-aquae bloom. Concentrations of inorganic P were determined
in extraction solutions of MgCl2 (1 M, pH 8), citrate-dithionite-bicarbonate, and 1 M HCl. Sediments
below 2 cm were dominated by residual P which is defined as total P minus inorganic P. During the study period, data from the top 2-cm of sediment indicated (a) significant decrease in total P concentration,
primarily associated with iron oxyhydroxides at one site, and (b) significant increase in total P concentration associated with residual P at a second site. Data from two other sites indicated no net changes in concentrations of total P.

Suspended-sediment and total phosphorus loads were computed for two sites in the Upper Klamath Basin on the Wood and Williamson Rivers, the two main tributaries to Upper Klamath Lake. High temporal resolution turbidity and acoustic backscatter data were used to develop surrogate regression models to compute instantaneous concentrations and loads on these rivers. Regression models for the Williamson River site showed strong correlations of turbidity with total phosphorus and suspended-sediment concentrations (adjusted coefficients of determination [Adj R2]=0.73 and 0.95, respectively). Regression models for the Wood River site had relatively poor, although statistically significant, relations of turbidity with total phosphorus, and turbidity and acoustic backscatter with suspended sediment concentration, with high prediction uncertainty. Total phosphorus loads for the partial 2014 water year (excluding October and November 2013) were 39 and 28 metric tons for the Williamson and Wood Rivers, respectively. These values are within the low range of phosphorus loads computed for these rivers from prior studies using water-quality data collected by the Klamath Tribes. The 2014 partial year total phosphorus loads on the Williamson and Wood Rivers are assumed to be biased low because of the absence of data from the first 2 months of water year 2014, and the drought conditions that were prevalent during that water year. Therefore, total phosphorus and suspended-sediment loads in this report should be considered as representative of a low-water year for the two study sites. Comparing loads from the Williamson and Wood River monitoring sites for November 2013–September 2014 shows that the Williamson and Sprague Rivers combined, as measured at the Williamson River site, contributed substantially more suspended sediment to Upper Klamath Lake than the Wood River, with 4,360 and 1,450 metric tons measured, respectively.

To support the development of Total Maximum Daily Load (TMDL) programs for the Klamath River in south-central Oregon and northern California, flow and water-quality models were developed by Tetra Tech for the U.S. Environmental Protection Agency, the Oregon Department of Environmental Quality (ODEQ), and the California North Coast Regional Water Quality Control Board. The EFDC model was used to simulate conditions in the Klamath River estuary, the RMA-2 and RMA-11 models were used to simulate most riverine reaches, and the CE-QUAL-W2 model was used to simulate the reservoir reaches. The U.S. Geological Survey (USGS) was asked to review only the most upstream of these models of the Klamath River, from its source at Upper Klamath Lake (Link River Dam) through its first pooled reach ending at Keno Dam.

The model developers have constructed streamflow and water-quality models to simulate a river reach that has highly complex water-quality processes that are not yet fully understood, and the models have great potential to help managers and regulators better understand the system. Certain errors identified in this review, however, need to be addressed before these models can be confidently used to predict temperature or water quality in the Link River Dam to Keno Dam reach of the Klamath River.

Poor water quality from hypereutrophic Upper Klamath Lake in south central Oregon has been suspected of contributing to the recruitment failure of two endangered endemic fish species. The Lost River sucker (Deltistes luxatus)and the shortnose sucker (Chasmistes brevirostris). We used otolith daily increment widths as a proxy for juvenile somatic growth to construct two growth models: (I) a linear mixed-effects (LME) model examining the lifetime effects of lakewide averages of potentially stressful daytime water temperature, pH. and nighttime dissolved oxygen (DO). and (2) a simple linear regression model examining the effects of locally measured water temperature. pH. and daytime DO on growth or fish over 3 d before the fish 's capture. Graphical relationships between daily growth and biweekly un-ionized ammonia failed to show a sublethal effect on the growth of suckers captured in areas where un-ionized ammonia surpassed levels lethal to both species. For both species , our LME models indicated that at temperatures greater than approximately 22°C, low nighttime DO (less than 4 mg/L for Lost River suckers and less than 1 mg/L for shortnose suckers) caused enough stress to reduce growth. whereas at temperatures less than approximately 22 C, any stress from low nighttime DO was not reflected in reduced growth. We attribute the pattern to the species tolerance of low D O. the short duration of nighttime events, the fish's increased oxygen demand at higher temperatures, and growth compensation due to increased food resources associated with low DO. The combination of low DO and high temperature has also been implicated in adult fish kills in Upper Klamath Lake. Because 34% of the time lakewide August average temperatures exceeded 22°C, extended periods of warm temperatures and high primary production could affect the sizes or recruits surviving into fall. Both growth models suggested that shortnose might be more tolerant of poor water quality than Lost River suckers.

This study evaluated the streamflow and nutrient dynamics of the Sprague River Basin over the period WY2002 – 2014 using biweekly flow and nutrient measurements collected by Klamath Tribes at eight sampling stations across the basin. Continuous daily time series of flows, loads, and concentrations were computed using methodologies similar to those used in a previous nutrient budget study of the entire Klamath Basin (Walker et al., 2012). These daily time-series were used as a basis to investigate the spatial and temporal dynamics of nutrient concentrations and loads, estimate relative amounts of background and anthropogenic loading, and evaluate long-term trends at each sampling station.

Distinguishing between anthropogenic and natural sources of sediment and nutrients is important for water resource management in irrigated basins. Water quality of flood irrigation was monitored at the field scale in the upper Klamath Basin, Oregon, on two unfertilized cattle pastures that were 2 ha (Site 1) and 70 ha (Site 2) in area. Water samples were analyzed for concentrations of sediment, total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), orthophosphate, ammonium-N (NHz 4 -N), and nitrate-N (NO{
3 -N). At both sites the TDN concentration was significantly greater in surface runoff than in applied irrigation water (P,0.05). Site 1 sediment and TDP concentrations were significantly greater in irrigation
surface runoff than in applied irrigation water (P,0.05). A first flush during irrigation was observed at Site 1 where nutrient concentration was at maximum value during the first 3 h of surface runoff. At Site 2 the surface runoff sediment and TDP concentrations were not significantly (P.0.05) higher than the applied irrigation, except when cattle were present. When export was measured, the mean yield of sediment and TDN per irrigation was 23.9 kg N? ha21 and 0.26 kg N? ha21, respectively, and there was a net retention of TDP of 0.04 kg P ? ha21. NHz 4 -N export occurred during one irrigation event yielding 0.15 kg N? ha21. NO{ 3 -N export was minimal or undetected. A late summer storm event resulted in pasture surface runoff concentrations of TDN and TDP that were 33 and 3 times higher, respectively, than irrigation source water concentrations. The TDN was significantly higher in subsurface runoff than it was in applied irrigation water (P,0.05). Improved irrigation efficiency might prevent many of the nutrient and sediment transport mechanisms observed during this study.

Current eutrophication models typically are used to predict seasonal mean conditions. However, the risk of
summer fish kills in hypereutrophic lakes is likely to be more closely dependent on periodic extreme events, such as potentially lethal peaks in pH driven by algal photosynthesis. In hypereutrophic Upper Klamath and Agency lakes, Oregon, peak summertime pH values frequently exceed critical levels that can reduce fish growth and survival (pH > 9.50, a likely sublethal tolerance limit for two resident endangered fish species). We developed two empirical models, one parametric and one nonparametric, that predict the likelihood of exceeding user-defined critical values of pH from concentrations of chlorophyll a in these lakes. Separate models were derived to incorporate seasonal dynamics and differences between the two lakes, and the behavior of these models was tested under four different critical pH scenarios. Both parametric and nonparametric models performed similarly, suggesting that management efforts to reduce chlorophyll a in these lakes from 200 to 100 μg·L–1 should decrease the probability of exceeding pH 9.5 by 45%. We suggest that this general approach potentially can be applied to the management of fish populations in other hypereutrophic lakes as well.

Large blooms of cyanobacteria, primarily Aphanizomenon flos-aquae, are linked to poor water quality in Upper Klamath Lake,
Oregon. High pH and high un-ionized ammonia concentrations are associated with the blooms when algae are actively growing,
followed by low dissolved oxygen (DO) conditions when the blooms decline in mid- to late summer. Over a 12-year study period,
algal biomass was strongly related to total phosphorus concentration (TP) and pH. Minimum water column DO was strongly related
to net negative changes (i.e., declines) in algal biomass during July and August. The severity of both low DO and high ammonia
was positively related to water column stability, which was dependent on wind speed. Bloom dynamics, coupled with climate,
dominated year-to-year variability in water quality dynamics in Upper Klamath Lake. These data provide the empirical basis for
previous research linking high mortalities of endangered sucker species with years of low wind and high water column stability.

The Sprague River CEAP study was designed to provide information about conservation practices through field monitoring and computer model simulations of the hydrologic budget. The Danish Hydrologic Institute's MIKE SHE hydrologic model was selected as the most appropriate hydrologic software. The MIKE SHE, an integrated hydrological modeling system, covers the entire land phase of the hydrological cycle, linking surface runoff with channel hydraulics and ground water hydrology.

This report constitutes the deliverable for Task 3 ("Assessment of the Klamath Estuary Spit") in the Estuary Technical Group's (ETG's) contract with the Yurok Tribe executed April 18, 2016. The contracts' goal is for ETG to assist the Tribe with coastal resource and climate change adaptation planning for the Klamath River Estuary. The original Scope of Work developed by the Tribe for the contract focused strongly on recommendations for improvements to the "Sea Level Affecting Marshes Model" ("SLAMM") for the Klamath River Estuary.

However, during the kick-off meeting in May 2016, the Tribe expressed its interest in thinking more broadly about ways to approach potential impacts of climate change to the estuary, rather than focusing on SLAMM. In subsequent discussions with the Tribe this was re-emphasized. For example, rather than developing data recommendations specifically to improve SLAMM as described in Task 1 ("Data and Model Review"), it was agreed that the ETG team would deliver broader data recommendations for improving the Tribe's ability to understand potential estuary habitat responses to climate change. These recommendations would constitute a combined deliverable for Tasks 1 and 2 (Task 2: "Data recommendations") which would be delivered after the Tribe's planned Klamath Estuary Workshop to be held in January 2018. As an initial step towards this combined deliverable, the ETG team delivered monitoring recommendations on July 7, 2016. Results of the recommended monitoring would support the Tribe's climate change adaptation planning in several ways: for example, the results could be used to support development of estuary habitat maps and models (including SLAMM if desired), and to improve general understanding of estuary conditions.

The purpose of this study was to investigate concerns identified by the Yurok Tribal membership about the health and safety of Yurok Waters, the Klamath River, and key aquatic species relied upon for culture, subsistence and economic benefits. Community concerns were identified in surveys conducted by YTEP in 2007 and the grant was funded by EPA National Center for Environmental Research in 2008. A large component of the study was sample and test selected aquatic species for a range of contaminants that could impact resource and human health, including heavy metals, pesticides and bio-toxins.

The Klamath Network (KLMN) is one of 32 National Park Service (NPS) networks responsible for developing vital signs-based monitoring programs for managing the longterm ecosystem health of the nation’s parks. The park units of the Klamath Network are Crater Lake National Park (CRLA), Lassen Volcanic National Park (LAVO), Lava Beds National Monument (LABE), Oregon Caves National Monument (ORCA), Redwood National and State Parks (RNSP), and Whiskeytown National Recreation Area (WHIS). National Park Service networks are required to formulate Vital Signs Monitoring Plans, consisting of three phases: Phase I compiles background information and data on network park unit resources and presents conceptual models for each park unit ecosystem; Phase II provides an augmented Phase I and the selection and prioritization of vital signs; and Phase III will include the entire scope of information in Phases I and II, as well as the monitoring objectives, sampling designs and protocols, and data management and analysis procedures of a long-term vital signs monitoring program. The Klamath Network Phase II Water Quality Report is intended to provide an overview of the previous water quality related inventory and monitoring work conducted in each of the network’s six park units and provide guidance in the direction of future monitoring objectives. The Phase II Report summarizes the activities undertaken to select vital signs to be used for monitoring the aquatic resources of Klamath Network park units.

This study is a screening study, providing a ‘snap-shot’ of existing conditions during the research years of 2009-2013. A brief summary of the project’s research methodology is offered here. (See Grant RD-83370801-0, Quality Assurance Project Plan for an in depth description of methods.)

This study was conducted in a multi-year, phased approach and includes both the review and consideration of pre-existing, secondary data (surveys, archival documents, ethnographic interviews, GIS databases, and environmental data on pesticide use) and the collection of primary new data generated through interviews, public participation geographic information system sessions, and chemical screening of surface water and tissue samples from targeted species. The first year involved review of previous data, community scoping and planning, the second and third years, public participation sessions, two tiers of field sampling, and laboratory analysis. The fourth and fifth years comprised data analysis and reporting.

The long-term sampling protocol for wadeable streams in the Klamath Inventory and Monitoring Network is the result of a collaborative effort of park personnel and the Network staff. This protocol covers five of the six Network park units: Crater Lake National Park, Oregon Caves National Monument, Lassen Volcanic National Park, Redwood National and State Parks, and Whiskeytown National Recreation Area. Lava Beds National Monument is not covered due to lack of surface water resources.
Key steps covered in the narrative include a brief history of ―water quality‖ monitoring and justification for use of key parameters as biomonitoring tools.
An always revisit panel design was chosen over more complicated designs based on: (1) Logistics of site establishment, (2) Trend detection, (3) Conceptual simplicity, and (4) Ease of data analysis. Sampling will occur every three years, in an alternating cycle. Cycle one will include the sampling of Whiskeytown National Recreation Area followed by Lassen Volcanic National Park. Cycle two, in the following year, will include sampling in Oregon Caves National Monument, followed by Redwood National and State Parks and conclude in Crater Lake National Park. This follows a pattern of sampling in lower elevational units early in the season, followed by the higher elevational parks. Target sample size is 30 stream reaches in every park, except Oregon Caves National Monument with a total of three stream reaches.

The long-term sampling protocol for mountain lakes and ponds in the Klamath Inventory and Monitoring Network is the result a collaborative effort of park personnel, USGS aquatic ecologist, and the Network staff.
Key steps covered in the narrative include a brief history of ―water quality‖ monitoring and justification for use of key parameters as biomonitoring tools. Invertebrates and plankton can respond to short-term impacts, while fish and amphibians can show long-term signals. The background of sampling done prior to this protocol in both Lassen Volcanic National Park and Crater Lake National Park is also covered; sampling at Lassen Volcanic National Park has been sporadic, and Crater Lake has been studied and monitored extensively, but is outside the scope of this particular protocol. The narrative links the methodology developed here to both national (e.g., United States Environmental Protection Agency and United States Geological Survey) methods and other Inventory and Monitoring Networks methods (e.g., North Coast Cascades Network). In sum, methods have been kept as comparable as possible, even though sampling designs and revisit patterns vary among national and NPS programs.
An always revisit panel design was chosen over more complicated designs based on: (1) Logistics of site establishment, (2) Trend detection, (3) Conceptual simplicity, and (4) ease of data analysis. Thirty sites will be monitored every three years at Lassen Volcanic National Park, and between six and ten sites will be sampled at Crater Lake National Park. Sampling will commence in 2013. Sampling will occur in summer, after snowmelt; starting at Lassen Volcanic National Park and then in Crater Lake National Park. One lagoon in Redwood National and State Parks will be sampled at the conclusion of the season.

The Klamath Basin in California and Oregon is a diverse and productive region that supports numerous ecological, economic, and cultural benefits. However, competing uses and major changes to the Basin’s hydrology have severely impacted the natural resources of the region. Efforts are underway for major restoration activities within the basin, with the goal of better balancing the diverse use of land and water resources. However, the myriad of ecological stressors on the basin’s resources can complicate predicting the trajectory and success of restoration efforts, thus it is important to inventory those stressors and identify critical data gaps prior to implementing actions. The Klamath Basin (approximately 31,000 square kilometers) has a relatively well‐documented history of contaminant impacts associated with historical pesticide use on agricultural lands. Agriculture accounts for approximately 6 percent of the land use in the entire basin, most of which exists in the Lost River, Shasta River, and Upper Klamath Lake subbasins (59, 14, and 11 percent, respectively). However, a current inventory of available data on contaminant distribution and sources is lacking. Thus, the goal of this document is to summarize what is currently known about past and current contaminant distribution and impacts of contaminants on the ecological communities throughout the basin. Additionally, we identify key data gaps which, when addressed, will facilitate a more thorough understanding of the factors driving contaminant cycling and ecological exposure so that efforts can be implemented to help minimize the threats.

Cataloging biodiversity is of great importance given that habitat destruction has dramatically increased extinction rates. While the presence of cryptic species poses challenges for biodiversity assessment, molecular analysis has proven useful in uncovering this hidden diversity. Using nuclear microsatellite markers and mitochondrial DNA we investigated the genetic structure of Klamath speckled dace (Rhinichthys osculus klamathensis), a subspecies endemic to the Klamath–Trinity basin. Analysis of 25 sample sites
within the basin uncovered cryptic diversity including three distinct genetic groups: (1) a group that is widely distributed throughout the Klamath River mainstem and its tributaries, (2) a group distributed in the Trinity River, the largest tributary to the Klamath River, and (3) a group identified above a 10 m waterfall in Jenny Creek, a small tributary to the Klamath River. All groups were resolved as divergent in nuclear microsatellite analysis and exhibited levels of divergence in mitochondrial DNA that were comparable to those observed among recognized Rhinichthys species. No physical barriers currently separate the Klamath and Trinity groups and the precise mechanism that generated and maintains the groups as distinct despite contact and hybridizationis unknown. The present study highlights the importance of incorporating molecular analysis into biodiversity research to uncover cryptic diversity. We recommend that future biodiversity inventories recognize three genetically distinct groups of speckled dace in the Klamath–Trinity Basin.

This paper explores the history of gold mining, gravel mining, and river restoration activities on the upper 42 miles of Trinity River, CA between Lewiston Dam and the North Fork Trinity River. Newly developed quantitative estimates of the sediment supply impacts associated with these activities are presented. Intensive hydraulic mining since the 1860’s has contributed vast amounts of sediment to the Trinity River. Contributions from the La Grange mine alone were sufficient to aggrade the valley bottom by over 3 feet. The longitudinal profile shows preliminary evidence of a persistent sediment wave resulting from hydraulic mining activities. Subsequent dredger mining overturned more than 70 percent of the floodplains. Historic gravel mining operations likely extracted between 60,000 and 125,000 cubic yards of gravel from the channel. A surprising result of this research is that river restoration activities over the last 40 years have extracted nearly as much gravel from the channel as they have augmented – roughly 90,000 cubic yards. Repeat bulk sampling between 2001 and 2009 showed reductions of up to 50 percent in the sand content of the substrate. Additional studies are underway to better understand the legacy impacts of mining and river restoration activities on the fluvial geomorphology and channel complexity of the Trinity River.

Listed as endangered in 1988, the Lost River sucker (Deltistes luxatus) and Shortnose sucker (Chasmistes brevirostris) were once abundant and widely distributed in the Klamath Basin in Southern Oregon and Northern California. Populations of both species have been declining since the late 1960’s. Factors thought responsible for declines include naturally occurring disturbances (e.g., periodic drought), water resource and land development activities, degradation of habitat and water quality, and interactions with introduced exotic species. Detection of any substantial adult recruitment for the last few decades has been minimal. We used a quantitative decision modeling approach to explore potential outcomes of alternative conservation strategies that include captive propagation and catch, grow, and release. Uncertainty about the factors responsible for the apparent lack of recruitment was represented using alternative models of system dynamics. Sensitivity analysis indicated that the model predictions were highly sensitive to population dynamics during early life stages and the alternative ideas of system dynamics. To address these uncertainties, I propose an adaptive approach to sucker recovery that integrates monitoring, research, and management.

With the decline of bull trout (Salvelinus confluentus), managers face multiple, and sometimes contradictory, management alternatives for species recovery. Moreover, effective decision-making involves all stakeholders influenced by the decisions (such as Tribal, State, Federal, private, and non-governmental organizations) because they represent diverse objectives, jurisdictions, policy mandates, and opinions of the best management strategy. The process of structured decision making is explicitly designed to address these elements of the decision making process. Here we report on an application of structured decision making to a population of bull trout believed threatened by high densities of nonnative brook trout (S. fontinalis) and habitat fragmentation in Long Creek, a tributary to the Sycan River in the Klamath River Basin, south-central Oregon. This involved engaging stakeholders to identify (1) their fundamental objectives for the conservation of bull trout, (2) feasible management alternatives to achieve their objectives, and (3) biological information and assumptions to incorporate in a decision model. Model simulations suggested an overarching theme among the top decision alternatives, which was a need to simultaneously control brook trout and ensure that the migratory tactic of bull trout can be expressed. More specifically, the optimal management decision, based on the estimated adult abundance at year 10, was to combine the eradication of brook trout from Long Creek with improvement of downstream conditions (for example, connectivity or habitat conditions). Other top decisions included these actions independently, as well as electrofishing removal of brook trout. In contrast, translocating bull trout to a different stream or installing a barrier to prevent upstream spread of brook trout had minimal or negative effects on the bull trout population.

The Klamath River and some of its tributaries are designated on the Clean Water Act (CWA) Section 303(d) list as impaired water bodies. Water quality is a concern in the Klamath River because it affects culturally and economically important salmon fisheries as well as public health. During the summer months, photosynthesis by aquatic plants and algae attached to the streambed elevate dissolved oxygen (O2) concentrations during the day, creating a 24-hour cycle in dissolved O2 concentrations. Respiration at night by those same organisms and bacteria has the reverse effect, depressing dissolved O2 levels. Resulting low nighttime dissolved O2 concentrations can exceed water quality standards and be stressful to fish (NCRWQCB 2010).

Ecosystem metabolism describes the fixation of organic carbon (gross primary production, GPP) and the mineralization of organic carbon (ecosystem respiration, ER). GPP and ER are integrative measures of river ecosystem health, and are complementary to more commonly used structural metrics that are regularly monitored on the Klamath River, such as dissolved O2 concentration, water temperature, and periphyton biomass. Ecosystem metabolism directly controls dissolved O2 concentrations in aquatic ecosystems and algal biomass, in part, forms the base of animal productivity in river food-webs (Thorp and Delong 2002, Cross et al. 2013).
Time series of daily metabolism estimates across many years allows examination of controls on metabolism at multiple time scales. Knowing what drives metabolism in the Klamath River will allow us to predict how rates of GPP and ER, and in turn, dissolved O2 concentrations will respond to changes in environmental conditions and management actions. Additionally, rates and patterns in ecosystem metabolism may be useful explanatory variables in other studies conducted in the Klamath River.

Klamath River is described as an “upside-down” river due to its origins from the hypereutrophic Upper Klamath Lake (UKL) and hydrology that is heavily regulated by upstream dams. Understanding the lake and reservoir effects on benthic communities in the river can inform important aspects of itswater quality dynamics. Periphyton samples were collected in May–November from 2004, 2006–2013 at nine long-term monitoring sites along 306 river km below UKL and a series of dams (n = 299). Cluster analysis of periphyton assemblages identified three statistically different periphyton groups (denotedGroups 1–3). Group 1 occurred primarily in the upstream reach for June–October and had a higher percentage of sestonic species, including the cyanobacteria Aphanizomenon flos-aquae and Microcystis aeruginosa, consistent with the presence of upstream reservoirs. Group 2 had the highest relative biomass of diatoms and lowest relative biomass of cyanobacteria. Sites in the lower reach of the Klamath River fell into Group 2 inMay–June and transitioning into Group 3 for July–October. Group 3 was dominated by nitrogen (N)-fixing species, including three diatoms (Epithemia sorex, Epithemia turgida, and Rhopalodia gibba) with cyanobacterial endosymbionts and the cyanobacterium Calothrix sp. Periphyton assemblages were strongly associated with temporal variations in flow conditions (e.g., decreasing flow from spring to fall) and spatial gradients in nutrient concentrations (e.g., decreasing from upstream to downstream). The inverse longitudinal relationship between periphyton biomass and nutrients may be explained by the ability of benthic N-fixers (Group 3) to overcome N limitation. Overall results showed a strong inverse relationship between the relative biomass of N-fixers and nitrogen concentrations and flow. This long-term dataset provides valuable insight into Klamath River's seasonal and longitudinal patterns of benthic algal communities and associated environmental variables.

Sediment-phosphorus release rates as a function of pH were determined in laboratory experiments for sediment and water samples collected from Shoalwater Bay in Upper Klamath Lake, Oregon, in 2001. Areal release rates for a stable sediment/water interface that is representative of the sediment surface area to water column volume ratio (1:3) observed in the lake and volumetric release rates for resuspended sediment events were determined at three different pH values (8.1, 9.2, 10.2). Ambient water column pH (8.1) was maintained by sparging study columns with atmospheric air. Elevation of the water column pH to 9.2 was achieved through the removal of dissolved carbon dioxide by sparging with carbon dioxide-reduced air, partially simulating water chemistry changes that occur during algal photosynthesis. Further elevation of the pH to 10.2 was achieved by the addition of sodium hydroxide, which doubled average alkalinities in the study columns from about 1 to 2 milliequivalents per liter. Upper Klamath Lake sediments collected from the lake bottom and then placed in contact with lake water, either at a stable sediment/water interface or by resuspension, exhibited an initial capacity to take up soluble reactive phosphorus (SRP) from the water column rather than release phosphorus to the water column. At a higher pH this initial uptake of phosphorus was slowed, but not stopped. This initial phase was followed by a reversal in which the sediments began to release SRP back into the water column. The release rate of phosphorus 30 to 40 days after suspension of sediments in the columns was 0.5 μg/L/day (micrograms per liter per day) at pH 8, and 0.9 μg/L/day at pH 10, indicating that the higher pH increased the rate of phosphorus release by a factor of about two. The highest determined rate of release was approximately 10% (percent) of the rate required to explain the annual internal loading to Upper Klamath Lake from the sediments as calculated from a lake-wide mass balance.

California has, or had, 32 distinct kinds of salmonid fishes. They are either endemic to California or at the southern end of their ranges. Most are in serious decline: 45% and 74% of all salmonids will likely become extirpated from California in the next 50 and 100 years, respectively, if present trends continue. Our results suggest that California will lose more than half (52%) of its native anadromous salmonids and nearly a third (30%) of its inland taxa in just 50 years under current conditions. Climate change is a major overarching threat driving population declines throughout California and strongly affects the status of 84% of all salmonids reviewed. In addition, dams, agricultural operations, estuary alteration, non-native species, production hatcheries, and myriad other human-induced threats have contributed to declines. 81% of salmonids in California are now worse off than they were in 2007, when the previous version of this report was prepared. The changes in species status are the result of the 2012-2016 historic drought, improved data collection and review, and an improved understanding of climate change impacts. Returning these iconic species to sustainable levels requires access to productive and diverse habitats which promote the full range of life history diversity necessary to weather change. We recommend (i) protecting and investing in fully functioning watersheds such as the Smith River and Blue Creek, (ii) protecting and restoring source waters such as Sierra meadow systems, groundwater, and springs so that the impacts of climate change are reduced, (iii) restoring function and access to once productive and diverse habitats such as Central Valley floodplains, coastal lagoons, and estuaries, (iv) adopting reconciliation ecology as a basis for management in human dominated landscapes, (v) improving habitat connectivity and passage to historical spawning and rearing habitat, and (vi) improving salmonid genetic management throughout California.

Interdisciplinary teams of Center scientists are investigating the causes for the decline of salmon and steelhead in Shasta River, historically one of the most productive tributaries in the lower Klamath Basin. A large spring complex (Big Springs Creek) provides the majority of its water, particularly during the summer.

Researchers are developing innovative approaches to restoring and sustainably managing this unique resource for both native fish and for irrigating local ranches and farms.

Though Shasta River provides only 1 percent of the Klamath River’s streamflow, it historically produced 50 percent of the Chinook salmon -- and it still produces enough fish to support a large proportion of California’s commercial and recreational salmon fishery. Improving freshwater habitat in the Shasta results in disproportionally large benefits for the lower Klamath Basin.

Hypereutrophic Upper Klamath Lake has been studied for almost 50 years to evaluate the nature, cause, and effects of its very productive waters. Mitigation of undesirable effects of massive cyanobacterial blooms requires understanding their modern causes as well as their history. Knowledge of the pre-settlement natural limnology of this system can provide guidelines for lake restoration and management of land and water use strategies to maximize the benefits of this aquatic resource. This investigation uses a paleolimnological approach to document the nature and chronology of limnological and biological changes in Upper Klamath Lake for the past 200 years, covering the time when the lake was first described until today. A 45-cm gravity core, dated by 210Pb and diatom correlations, was analyzed for diatoms, pollen, akinetes (resting spores) of the cyanobacterium Aphanizomenon flos-aquae, reworked tephra shards, and sediment magnetic characteristics. Pollen profiles show little vegetation change during this time. In contrast, diatoms indicative of increased nutrient fluxes (P and Si) increase moderately, coinciding with the settlement of the region by Euro-Americans. Numerous settlement activities, including draining of lake-margin marshes, upstream agriculture and timber harvest, road construction, and boat traffic, may have affected the lake. Magnetic properties and reworked tephra suggest riparian changes throughout the basin and increased lithogenic sediment delivery to the lake, especially after 1920 when the marshes near the mouth of the Williamson River were drained and converted to agricultural and pasture land. Drainage and channelization also decreased the ability of the marshes to function as traps and filters for upstream water and sediments. Akinetes of Aphanizomenon flos-aquae record progressive eutrophication of Upper Klamath Lake beginning in the 20th century and particularly after 1920 when lake-margin marsh reclamation more than doubled.

Many wetland restoration projects are initiated with phosphorus (P) retention as a primary objective. While undisturbed wetlands often are net sinks for P and other nutrients, there is evidence that newly flooded restoration wetlands on former agricultural land initially release P to surface waters. The objectives of this study were to: 1) measure P release from soils to overlying surface waters that would occur when re-flooding agricultural fields to restore a lake fringe wetland connected to Upper Klamath Lake, Oregon; and 2) identify management strategies to abate nutrient release from soils during restoration to minimize P loading to Upper Klamath Lake. We simulated the process of re-flooding soils using mesocosms in a laboratory experiment. The soils were flooded with lake water, and the water was replenished on a weekly basis. The net P flux from soils to surface water was estimated by measuring differences in P concentrations between water that had been in the mesocosms and the lake water used for replenishment. After the flooding experiment, we measured the concentrations of four forms of soil P using a modification of the Hedley procedure, to examine relationships between soil P chemistry and P release. The majority of P was released in the first two days of the experiment, and all detectable P was released by the end of the second month. We estimated that 1–9 g P/m2 were released from the soils to the water column over the course of the experiment, which amounted to 1%–16% of total soil P. Scaling up to the entire wetland, this totals approximately 64 tons P released over 3,000 ha. We did not find any statistically significant relationships between any of the four forms of soil P and the amount of P released in the flooding experiment.

Integrated Water Resources Management (IWRM) is one of the most utilized models in water policy and administration. One of the crucial components in IWRM is collaboration, where multiple stakeholders negotiate solutions. This article explores the role of collaboration in one of the most contentious water conflicts in the nation—the Klamath River. The range of stakeholders is enormous and complex, including Indian tribes, farmers, fishermen, recreationists, environmentalists, advocates of endangered species, two states, and multiple federal agencies. The parties in the Klamath Basin negotiated three settlements to resolve many of the major issues. However, the U.S. Congress failed to approve the settlements in late 2015, effectively ending this long-term effort to resolve these vexing issues through collaborative negotiations. This conflict is analyzed using a multi-method approach, and discusses how the failure of the settlement process can provide insights into the role of collaboration in IWRM, and suggests refinements to the model.

Fisheries and Oceans Canada requires escapement goals for Chinook salmon (Oncorhynchus tshawytscha) stocks to evaluate their status and achieve objectives established by international agreements and domestic policy. Unfortunately the data typically needed to establish these ‘goals’, using stockrecruitment techniques, are expensive to gather and are, for most stocks, lacking. This prompted us to develop the habitat-based approach to generate escapement goals described in this report.

We related productive capacity to freshwater habitat area based on results from a meta-analysis of 25 Chinook stocks. Stocks were distributed between central Alaska and northern Oregon and represented a broad range of environments and life history. We developed an allometric model that predicted Smsy and Srep (spawners required to produced maximum sustained yield and replacement, respectively) from the watershed area and assessed the model’s performance. The model adequately predicted the Smsy and Srep for an independent data source and out-performed a current interim method applied to British Columbia (BC) Key Streams. The habitat-based approach adequately predicted Smsy and Srep for seven case study examples, although it overestimated the productive capacity of stocks with relatively small spawning areas.

Our habitat-based model can generate biologically-based escapement goals, rooted in fish-production relationships, for data limited stocks over a broad range of environments. This simple approach requires easily acquirable data and makes few assumptions. However, spawner escapements of known accuracy and reliability are required, which may impede implementation for some systems. The approach is wellsuited for most data limited stocks in BC and can be tested and refined as new stock-recruitment data become available.

This document is the Standard Operating Procedure (SOP) for collecting and field-processing stream algae for the California State Water Resources Control Board’s Surface Water Ambient Monitoring Program (SWAMP). Instructions are provided for the following:
• collection of samples for taxonomic identification of diatoms and soft-bodied algae
• collection of samples for determination of biomass based on chlorophyll a and ash-free dry mass (AFDM)
• estimation of percent algal cover

Bathymetric surveys were conducted on Lake Ewauna, Keno Reservoir, JC Boyle Reservoir, Copco Reservoir, and Irongate Reservoir. A supervised sediment classification was also conducted on each of these impoundments. A general assessment of the magnitude of accumulated sediment in the impoundments was conducted by comparing the current bathymetry of the impoundments with available information on pre-impoundment topography. The results indicate the sediment accumulation in the impoundments is relatively modest, generally ranging from 5 to 15 percent of the current volumes.

The authors tested the hypothesis that zooplankton diversity and density are affected by the presence of cyanotoxins in the water. The authors focused on 4 oxbow lakes of the Vistula River in southern Poland, which are subjected to mass cyanobacterial development. In 2 of the oxbows (Piekary and Tyniec), microcystins released into the water were found. The highest concentration of microcystins (0.246mg/L) was observed for microcystins LR. Zooplankton diversity showed a weak response to the presence of microcystins released into the water. The Shannon index (H’) of total zooplankton diversity decreased in the Piekary and Tyniec oxbows during periods when the microcystin concentrations were highest. The same trend was noted for diversity of rotifers in both oxbows and for diversity of copepods in Piekary, but not for copepods in Tyniec. No such trends were found for the diversity of cladocerans in any of the oxbows, nor was a relationship found between density of zooplankton and microcystins. Statistical analyses showed that the number of species in individual samples was negatively correlated with the levels of sulfates, phosphates, and ammonia, but the microcystin concentration was positively related to those levels. This points to the complexity of the interactions and synergies among toxins, abiotic factors, and zooplankton biodiversity. In focusing on the problem of cyanotoxins, conservation studies should pay attention to this complexity.
Environ Toxicol Chem 2017;36:165–174. # 2016 SETAC

Cyanobacteria, also known as blue-green algae, are a family of single-celled algae that proliferate in water bodies such as ponds, lakes, reservoirs, and slow-moving streams when the water is warm and nutrients are available. Many cyanobacteria species produce a group of toxins known as microcystins, some of which are toxic. The species most commonly associated with microcystin production is Microcystis aeruginosa. Upon ingestion, toxic microcystins are actively absorbed by fish, birds and mammals. Microcystin primarily affects the liver, causing minor to widespread damage, depending on t

The blue-green algae Microcystis aeruginosa can produce a family of toxins known as microcystins. They can cause liver damage that can lead to death in dogs and livestock. No known deaths have been reported in humans from the ingestion of microcystins. Fish and birds are also at risk for microcystin toxicity. Regardless of species, the mechanism of action is the same – the inhibition of protein phosphatase which causes primarily liver damage, but also affects other organs. Microcystins also act as a tumor promoter.

While microcystins are not as toxic as many natural toxins, they are becoming more and more ubiquitous in California, leading to greater opportunities for exposures. Microcystis blooms occur in quiet, warm waters that are nutrient-rich; the type of conditions that are found in lakes, reservoirs, dammed rivers, and even agricultural drainage ditches throughout the state.

Microcystins have also been detected in the Delta. Steps are being taken to begin to address this problem. In 2008, the Klamath River was added to the Clean Water Act’s 303d list as an impaired waterbody as a result of microcystis blooms. It appears that some dams on this river will be removed along the Klamath, which should reduce the frequency or possibly eliminate toxic blooms. Affirmative steps such as these will help reduce the risk of exposure and adverse effects associated with microcystins.

Cyanobacteria, also known as blue-green algae, are prokaryotic, phototrophic microorganisms that may form massive blooms in eutrophic water reservoirs. Some cyanobacterial strains are able to produce secondary metabolites – cyanotoxins that may be hazardous to aquatic and terrestial animals. These compunds can be grouped into: hepatotoxins, neurotoxins, cytotoxins dermatotoxins and irritant toxins. Microcystins are well-known cyclic heptapeptides acting as inhibitors of protein phosphatases type 1 and 2A. These cyanotoxins induce various adverse effects in freshwater invertebrates including biochemical, physiological and behavioral changes. Moreover, accumulation of microcystins in different tissues occurs, therefore transfer of these cyanotoxins through the food chain to animals being at higher trophic levels may be possible. The purpose of this paper is to review the knowledge on the effects of microcystins on three main groups of freshwater invertebrates: zooplankton, higher crustaceans, mollusks and to indicate possible ecotoxicological consequences of this impact on aquatic environment and invertebrate aquacultures.

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.

The primary objective of this Technical Support Document is to provide the California State Water Resources Control Board (SWRCB) and the Oregon Department of Environmental Quality (ODEQ) the information they require to prepare the Clean Water Act Section 401 Water Quality Certifications (401 Certifications) for the Lower Klamath Project, also referred to as the Klamath River Renewal Project (Project). The 401 Certifications are required before the Federal Energy Regulatory Committee (FERC) can issue a final surrender order for the Project. In addition, this document provides the latest available technical and field information developed by the Klamath River Renewal Corporation and its consultants (KRRC), for SWRCB’s use in preparation of an Environmental Impact Report (EIR) consistent with the California Environmental Protection Act (CEQA). The SWRCB and ODEQ communicated their specific information needs via letters dated August 24, 2017 and July 19, 2017, respectively. Copies of the Additional Information Request letters can be found in Appendix A.

Reintroduction of imperiled native freshwater fish is becoming an increasingly important conservation tool amidst persistent anthropogenic pressures and new threats related to climate change.We summarized trends in native fish reintroductions in the current literature, identified predictors of reintroduction outcome, and devised recommendations for managers attempting future native fish reintroductions. We constructed random forest classifications using data from 260 published case studies of native fish reintroductions to estimate the effectiveness of variables in predicting reintroduction outcome. The outcome of each case was assigned as a success or failure on the basis of the author’s perception of the outcome and on whether or not survival, spawning, or recruitment were documented during post-reintroduction monitoring. Inadequately addressing the initial cause of decline was the best predictor of reintroduction failure. Variables associated with habitat (e.g., water quality, prey availability) were also good predictors of reintroduction outcomes, followed by variables associated with stocking (e.g., genetic diversity of stock source, duration of stocking event). Consideration of these variables by managers during the planning process may increase the likelihood for successful outcomes in future reintroduction attempts of native freshwater fish.

As adaptive management becomes more widely recognized as a foundation element of good land stewardship, many resource professionals are attempting to extend its theories and principles into common practice. They wish to conduct powerful management experiments, to monitor the outcomes effectively and efficiently, and to use the resulting data to make reliable inferences for future decisions. Most managers, however, have little formal training in the application of experimental design and statistics to the problems that they want to address through adaptive management. This book sets the stage for the in-depth discussions of key aspects of statistics in adaptive management. It includes a working definition of adaptive management, demonstrates the value of the application of adaptive management to forestry issues, and explains some of the differences between research studies and adaptive management techniques.

Humans have dramatically altered landscapes as a result of urban and agricultural development, which has led to decreases in the quality and quantity of habitats for animals. This is particularly the case for freshwater fish that reside in fluvial systems, given that changes to adjacent lands have direct impacts on the structure and function of watersheds. Because choices of habitat have physiological consequences for organisms, animals that occupy sub-optimal habitats may experience increased expenditure of energy or homeostatic overload that can cause negative outcomes for individuals and populations. With the imperiled and threatened status of many freshwater fish, there is a critical need to define relationships between land use, quality of the habitat, and physiological performance for resident fish as an aid to restoration and management. Here, we synthesize existing literature to relate variation in land use at the scale of watersheds to the physiological status of resident fish. This examination revealed that landscape-level disturbances can influence a host of physiological properties of resident fishes, ranging from cellular and genomic levels to the hormonal and whole-animal levels. More importantly, these physiological responses have been integrated into traditional field based monitoring protocols to provide a mechanistic understanding of how organisms interact with their environment, and to enhance restoration. We also generated a conceptual model that provides a basis for relating landscape-level changes to physiological responses in fish. We conclude that physiological sampling of resident fish has the potential to assess the effects of landscape-scale disturbances on freshwater fish and to enhance restoration and conservation.

Dams have been a fundamental part of the U.S. national agenda over the past two hundred years. Recently, however, dam removal has emerged as a strategy for addressing aging, obsolete infrastructure and more than 1,100 dams have been removed since the 1970s. However, only 130 of these removals had any ecological or geomorphic assessments, and fewer than half of those included before- and after-removal (BAR) studies. In addition, this growing, but limited collection of dam-removal studies is limited to distinct landscape settings. We conducted a meta-analysis to compare the landscape context of existing and removed dams and assessed the biophysical responses to dam removal for 63 BAR studies. The highest concentration of removed dams was in the Northeast and Upper Midwest, and most have been removed from 3rd and 4th order streams, in low-elevation (< 500 m) and low-slope (< 5%) watersheds that have small to moderate upstream watershed areas (10± 1000 km2) with a low risk of habitat degradation. Many of the BAR-studied removals also have these characteristics, suggesting that our understanding of responses to dam removals is based on a limited range of landscape settings, which limits predictive capacity in other environmental settings. Biophysical responses to dam removal varied by landscape cluster, indicating that landscape features are likely to affect biophysical responses to dam removal. However, biophysical data were not equally distributed across variables or clusters, making it difficult to determine which landscape features have the strongest effect on dam-removal response. To address the inconsistencies across dam-removal studies, we provide suggestions for prioritizing and standardizing data collection associated with dam removal activities.

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.

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.

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.

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)

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 (10–15
C) 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.

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.

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.

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.

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.

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.

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.

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.

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.

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 (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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 (29
40
1 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 (3
60
1 LF s1), Rr (20013 mg O2 kg0
830 h1) and metabolic power (53322 mg O2 kg0
882 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.

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.

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.

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)

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.

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, 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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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).

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.

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.

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.

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.

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).

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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%.

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.

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.

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.

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 24
C; (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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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%).

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%).

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.

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.

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.

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.

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.

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.

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.

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.

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).

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

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.

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.

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.

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.

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

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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).

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.

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.

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.

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.

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

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.

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.

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

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%).

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.

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.

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.

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.

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.

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.

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.

Website for Siskiyou County, California.

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."

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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).

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.

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.

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.

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

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.

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).

Klamath map showing the various areas of the Klamath Basin.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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,

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.

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.

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.”

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.