Multidecadal trends for three declining fish species: habitat patterns and mechanisms in the San Francisco Estuary, California, USA

We examined a 36-year record of concurrent midwater trawl and water quality sampling conducted during fall to evaluate habitat trends for three declining fish species in the San Francisco Estuary, California, USA: delta smelt (Hypomesus transpacificus), striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense). Generalized additive modeling revealed that Secchi depth and specific conductance were important predictors of occurrence for delta smelt and striped bass, while specific conductance and water temperature were important for threadfin shad. Habitat suitability derived from model predictions exhibited significant long-term declines for each species; the southeastern and western regions of the estuary exhibited the most dramatic changes. Declines in habitat suitability were associated with anthropogenic modifications to the ecosystem. For delta smelt, an imperiled annual species endemic to the estuary, the combined effects of fall stock abundance and water quality predicted recruit abundance during recent years of chronically low food supply. Our results are consistent with existing evidence of a long-term decline in carrying capacity for delta smelt and striped bass and demonstrate the utility of long-term data sets for evaluating relationships between fish and their habitat.