San Francisco Estuary and Watershed Science

Differing and confounding understandings of the seasonal movements of the delta smelt (Hypomesus transpacificus) in the San Francisco Estuary persist nearly 2 decades after its listing as threatened under the federal and state endangered species acts. The U.S. Fish and Wildlife Service and the U.S. Bureau of Reclamation have characterized the delta smelt as a species that migrates extensive distances from Suisun Bay and the Sacramento and San Joaquin rivers confluence in the fall and winter, eastward and upstream to the central and east Sacramento–San Joaquin Delta to spawn, with the next generation returning to downstream rearing areas in the following spring (OCAP Technical Support Team unpublished; USBR 2012). This description of inter-seasonal movements of delta smelt stands in contrast to findings drawn from previous studies, which describe movements by pre-spawner delta smelt from open waters in bays and channels to proximate marshlands and freshwater inlets (e.g., Moyle et al. 1992; Bennett 2005). In an effort to resolve this disagreement over the movements of delta smelt, we use publicly available data on its distribution drawn from trawl surveys to generate maps from which we infer seasonal patterns of dispersal. In the fall, before spawning, delta smelt are most abundant in Suisun Bay, the Sacramento and San Joaquin rivers confluence, the lower Sacramento River, and the Cache Slough complex. By March and April, the period of peak detection of spawning adults, relative densities in Suisun Bay and the rivers’ confluence have diminished in favor of higher concentrations of delta smelt in Montezuma Slough and the Cache Slough complex. A relatively small percentage of fish are observed in areas of the Sacramento River above Cache Slough. We conclude that inter-seasonal dispersal of delta smelt is more circumscribed than has been previously reported. This conclusion has real-world implications for efforts to conserve delta smelt. Our findings support a conservation strategy for delta smelt that focuses on habitat restoration and management efforts for tidal marsh and other wetlands in north Delta shoreline areas directly adjacent to open waters that have been documented to support higher concentrations of the fish.