Contrasting life-cycle impacts of stream flow on two Chinook salmon populations

Stream flow affects many aspects of freshwater fish biology, but the extent to which variation in stream flow influences productivity of anadromous salmonid populations across their entire life cycle is not well known. We compared relationships of stream flow and productivity for Chinook salmon (Oncorhynchus tshawytscha) from two systems in the Salmon River basin in Idaho: the Lemhi River, a watershed subjected to intensive water use for irrigation, and Marsh Creek, a drainage with a natural hydrograph. We estimated rates of productivity based on monitoring at four life stages: the number of eggs initiating each cohort, juveniles migrating from the natal tributary past an outmigrant trap, smolts surviving to the Snake River, and adults returning to spawn. Using model selection techniques, we examined whether river flow experienced during these life stages explained variation above and beyond predictors of climate associated with each stage. In the Lemhi River, tributary stream flow during early residence exhibited strong correlations with egg-trap, egg-smolt, and egg-adult return rates, and was consistently a better predictor of productivity than stream flow occurring during late summer. Model selection indicated that early rearing flow was the single best predictor of both egg-trap and trap-smolt transition rates in the Lemhi River, and path analysis revealed a strong set of pathways linking rearing flow to adult return rate primarily through egg-trap productivity. These patterns were much less strongly exhibited or nonexistent in Marsh Creek. However, for both populations, migration flow in the Columbia River was the best predictor of smolt-adult return rates. Potentially confounding climatic variables exhibited relatively weak effects upon both early life histories and tributary flow, but were included in the best models of migration flows and smolt-adult return rate. These results suggest that effects of stream flow on juvenile salmonids in flow-altered systems can have substantial impacts on returning adults.