San Francisco Estuary and Watershed Science

Climate change is having widespread negative effects on freshwater environments, including an increasing frequency and severity of droughts. Drought conditions present unique challenges for the federally listed Central Valley Chinook Salmon (Oncorhynchus tshawytscha), which use the already limited floodplain in the Central Valley as rearing habitat. In this study, we examined how differing hydrologic conditions influence the run composition of juvenile Chinook Salmon in the floodplain (Yolo Bypass) versus the mainstem of the Sacramento River. Juvenile Chinook Salmon from the Yolo Bypass and areas along the Sacramento River were identified to the genetically distinct runs (fall, late fall, winter, and spring) from 2013-2019. We found overwhelmingly that Length at Date methods are misclassifying fish, particularly late fall and spring run fish, and winter-run fish in the bypass. Using this genetic run-timing, we found that the abundances of endangered runs (spring and winter) are reduced during low flow periods in both the bypass and Sacramento River. Even during drought conditions, juvenile Chinook Salmon rearing in the Yolo Bypass attained significantly larger sizes than those in the Sacramento River. When comparing fish growth across time, during wet years fish in the bypass start smaller and get significantly larger over the course of the year as compared to drought years, while during both wet and dry years fish in the Sacramento River largely attain a smaller size than the Yolo Bypass fish. This suggests that floodplain habitat is critical to maintaining diversity in juvenile Chinook Salmon.