Relating survival of fall-run Chinook Salmon through the San Joaquin Delta to river flow

Survival of juvenile fall-run Chinook Salmon Oncorhynchus tshawytscha from the San Joaquin River (SJR) during their migration through the Sacramento-San Joaquin Delta of California has been low in recent years, and there is uncertainty about the role of river flow on survival. Five years (2010–2014) of acoustic telemetry data from juvenile hatchery-reared salmon offer spatially detailed survival information through this region. Multinomial regression and generalized linear models were used to relate survival to river flow in the SJR and its distributary, Old River (OR), on various spatial and temporal scales. Higher survival to Delta exit (rkm 77 from Golden Gate Bridge) was associated with higher root mean square of OR flow in the strongly tidal interior Delta (rkm 123; P < 0.0001), but not with higher SJR flow either entering the Delta from upstream (rkm 196; P = 0.2795) or measured in the Delta near the riverine/tidal interface (rkm 150; P = 0.3845). Survival in the upstream, more riverine region of the Delta was positively associated with SJR flow measured at rkm 150 and average net flow in the interior Delta (P ≤ 0.0001 for each), suggesting different mechanisms driving survival in the upstream versus downstream reaches of the Delta. The spatial complexity of the survival-flow relationship suggests that efforts to maximize total Delta survival should focus on a sequence of smaller regions, tailoring management strategies to each region rather than a single strategy for the Delta as a whole. Highly variable environmental conditions in this region combined with very low survival require more data to fully address the complex survival-flow relationship, both more years of data on various spatial scales and larger sample sizes of acoustic-tagged fish.