Differences among runs of Chinook Salmon in routing probability at the Georgiana Slough-Sacramento River junction

The survival of juvenile Chinook Salmon (Oncorhynchus tshawytscha) depends on the specific migration route they take through the Sacramento–San Joaquin Delta. Factors such as flow magnitude, flow direction, and distribution of fish across the channel significantly affect the likelihood of their entering routes with lower survival probabilities. Management strategies to mitigate the entry of endangered winter-run and threatened spring-run Chinook Salmon into the interior Delta—particularly through Georgiana Slough—involve flow regulation and the installation of a bioacoustic fish fence. Monitoring the effectiveness of these measures has primarily relied on acoustically-tagged, juvenile, hatchery-reared, late-fall-run Chinook Salmon, which are easier to obtain and can accommodate larger tags compared to other runs. Previous studies explored how flow dynamics affect routing probabilities of late-fall-run Chinook Salmon, but there is a lack of understanding about how routing probabilities vary among runs. We leveraged data from 15 previous studies comprising 3,004 acoustically-tagged fish across all four runs, over a 12-year period, to assess the effects of run on routing probability into Georgiana Slough, while accounting for variation in flow dynamics. We employed logistic regression to model the influence of tidal flow metrics, time of day (day and night), and run type on the probability of juvenile Chinook Salmon being routed into Georgiana Slough. Our analysis revealed that reverse flow during incoming tides influenced the routing probabilities of all runs. An increased proportion of flow into Georgiana Slough, meant an increased probability for all runs to be routed into Georgiana Slough. Late-fall-run Chinook Salmon also showed a greater probability of routing into Georgiana Slough during the night than during the day, whereas the opposite was true for other runs. These differences in routing probability affect our understanding of how management actions intended to reduce routing into Georgiana Slough may differentially affect the four runs of Chinook Salmon in the Sacramento River.