Hierarchical Modeling of Juvenile Chinook Salmon Survival as a Function of Sacramento-San Joaquin Delta Water Exports

A multiyear study was carried out in the Sacramento-San Joaquin Delta system to examine the relationship between the survival of out-migrating Chinook salmon Oncorhynchus tshawytscha and the amount of water exported from the system by the two major pumping stations in the southern portion of the delta. Paired releases of groups of coded-wire-tagged juvenile late-fall-run Chinook salmon were made at two locations in the delta, one in the main-stem Sacramento River and one in the interior portion of the delta where they were more likely to be directly affected by the pumping stations. Shortly after release, the fish were recovered downstream by a midwater trawl, and over a 2-4-year period the fish were recovered in ocean fishery catches and spawning ground surveys. A Bayesian hierarchical model for the recoveries was fit that explicitly accounted for the between-release variation in survival and capture probabilities as well as the sampling variation in the recoveries. The survival of the interior delta releases was considerably lower than that of main-steam releases (mean ratio of survival probabilities, 0.35). The ratio of survival probabilities was negatively associated with water export levels, but various model selection criteria gave more (or nearly equal) weight to simpler models that excluded exports. However, the signal-to-noise ratio, defined in terms of the export effect relative to environmental variation, was very low, and this could explain the indeterminacy in the results of the model selection procedures. Many more years of data would be needed to more precisely estimate the export effect. Whatever the factors that adversely affect survival through the interior delta, the fraction of out-migrants that enter the interior delta needs to be estimated in order to determine the overall effect of water exports on out-migrating Sacramento river Chinook salmon.