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.