Route use of emigrating steelhead in a heavily modified river delta

ObjectiveLow survival of emigrating salmonid smolts through the interior regions of California's Sacramento–San Joaquin River Delta (hereafter, “Delta”) and large‐scale water extraction from that region have prompted managers to seek to predict and manipulate smolt route use through the tidal Delta. The local flow variables previously used in modeling are not the metrics used in management. Here, I investigate the predictive utility of variables representing both localized flow conditions and remote management metrics to predict routing of juvenile steelhead Oncorhynchus mykiss at two river junctions on the San Joaquin River in the south Delta.MethodsIndividual‐based generalized linear models were used with detections of over 4000 acoustic‐tagged juvenile hatchery‐reared steelhead to relate routing to the presence of a rock barrier, simulated localized flow conditions from a hydrodynamic model, and daily management metrics, including upstream river discharge and water pumping rates elsewhere in the Delta. Models were developed for the first two diffluences encountered by smolts entering the Delta (head of Old River and Turner Cut).ResultExclusive use of the management metrics in routing models underestimated the subdaily, tidally dominated fluctuations in fish routing compared to localized flow covariates. The daily rate of water extraction 20–30 km away contributed to use of non‐main‐stem routes, but the effect was small compared to subhourly flow conditions at the river junctions themselves.ConclusionWater resource and fish managers are advised to monitor conditions at the locations of interest rather than depending solely on remote metrics. In the Delta, use of a flow barrier and reduction of water pumping operations when smolts are migrating should be combined with habitat improvement in interior Delta regions to optimize migratory survival through this complex and heavily modified system.