San Francisco Estuary and Watershed Science

We used a combination of published literature and field survey data to synthesize the available information about habitat use by delta smelt Hypomesus transpacificus, a declining native species in the San Francisco Estuary. Delta smelt habitat ranges from San Pablo and Suisun bays to their freshwater tributaries, including the Sacramento and San Joaquin rivers. In recent years, substantial numbers of delta smelt have colonized habitat in Liberty Island, a north Delta area that flooded in 1997. The species has a more upstream distribution during spawning as opposed to juvenile rearing periods. Post-larvae and juveniles tend to have a more downstream distribution during wetter years. Delta smelt are most common in low-salinity habitat (<6 psu) with high turbidities (>12 NTU) and moderate temperatures (7 °C to 25 °C). They do not appear to have strong substrate preferences, but sandy shoals are important for spawning in other osmerids. The evidence to date suggests that they generally require at least some tidal flow in their habitats. Delta smelt also occur in a wide range of channel sizes, although they seem to be rarer in small channels (<15 m wide). Nonetheless, there is some evidence that open water adjacent to habitats with long water-residence times (e.g. tidal marsh, shoal, low-order channels) may be favorable. Other desirable features of delta smelt habitat include high calanoid copepod densities and low levels of submerged aquatic vegetation (SAV) and the toxic algae Microcystis. Although enough is known to plan for large-scale pilot habitat projects, these efforts are vulnerable to several factors, most notably climate change, which will change salinity regimes and increase the occurrence of lethal temperatures. We recommend restoration of multiple geographical regions and habitats coupled with extensive monitoring and adaptive management. An overall emphasis on ecosystem processes rather than specific habitat features is also likely to be most effective for recovery of the species.