Predicting juvenile Chinook Salmon routing in riverine and tidal channels of a freshwater estuary

As juvenile salmonids migrate from natal streams to the ocean they can encounter junctions leading to migration routes that differ in quality and survival probability, including: side channels, agricultural diversions, floodplains, cooling intakes and turbines. Although juvenile salmon are known to use all these routes, it is often difficult to estimate what proportion of migrants may use each. Managers would benefit from knowledge of how hydrologic manipulation (e.g., dam releases, water diversions) can reduce exposure to unfavorable routes and keep more fish in higher survival routes. We assembled 41 estimates of juvenile salmon routing at six junctions in the Sacramento-San Joaquin Delta to test the ability of three hydrologic metrics to predict fish routing at distributary channels. The proportion of flow entering the distributary was selected as the best predictor and explained 70 % of observed variation in fish routing. This linear model was then used to predict routing at nine junctions under various combinations of inflow and exports. Our results suggest that more fish enter distributaries at junctions with strong riverine influence, whereas at tidally dominated junctions entrainment was lower. River inflow had the largest effect on entrainment at the two riverine-dominated junctions, although confidence intervals overlapped over the range of flows. Exports had a smaller than expected effect, but had the greatest effect at junctions directly connected to the channels with water diversions. These results suggest that flow proportion is an effective metric to predict fish routing. However, results also suggest it may be difficult to appreciably alter fish routing by manipulating river inflows or water diversions.