Hydraulic Microhabitats at a Regulated River Confluence Influence Chinook Salmon Migratory Routing During Drought

ABSTRACT Successful upstream adult migration of Pacific salmon ( Oncorhynchus spp .) from estuary to spawning grounds is critical to population recovery, especially during increasingly extreme droughts that degrade migratory habitat. In regulated systems, river confluences can pose significant navigation impediments given complex operational flow release criteria and other cumulative effects. Differing discharge magnitudes and ratios between tributaries may cause divergent confluence hydraulics and hydraulic microhabitat selectivity, influencing migratory routing. This study asks with respect to confluences: (1) Do magnitudes of discharge in each confluence tributary (and resulting combined discharge) influence availability of preferred hydraulic microhabitats in one river versus the other? (2) Does the ratio of discharge magnitudes influence availability of preferred hydraulic microhabitats in one river versus the other? We used data collected from California Central Valley fall‐run Chinook salmon ( Oncorhynchus tshawytscha ) at the confluence of the Feather and Yuba Rivers as a model system to investigate. We combined observations of migratory behavioural responses to hydraulic microhabitats from dual‐frequency identification sonars, spatially explicit, meter‐resolution hydrodynamic modelling, and machine learning to generate a hydraulic microhabitat selectivity index and simulate upstream migratory pathways for nine pertinent discharge scenarios with four discharge ratios. Statistically significant ( p < 0.01) differences in preferred hydraulic habitat were found among both discharge scenarios and ratios, with the Feather River selected in five out of nine scenarios. Discharge magnitude and ratio act as controls on distribution of preferred hydraulic microhabitats, and under certain conditions relevant to drought operations in this system, they can influence migratory routing and propensity of straying.