Longfin smelt: spatial dynamics and ontogeny in the San Francisco Estuary, California

We utilized recently available sampling data (similar to 1959-2012) from the Interagency Ecological Program and regional monitoring programs to provide a comprehensive description of the range and temporal and geographic distribution of longfin smelt (Spirinchus thaleichthys) by life stage within the San Francisco Estuary, California (Estuary). Within 22 sampling regions, we identified 357,538 survey events at 1,203 monitoring stations. A total of 1,035,183 longfin smelt (LFS) were observed at 643 stations (53%) in an area from Central San Francisco Bay (Tiburon) in the west, to Colusa on the Sacramento (Sacramento Valley region) in the north, Lathrop on the San Joaquin River (border of South Delta and San Joaquin River regions) to the east and South San Francisco Bay (Dumbarton Bridge) to the south, an area of approximately 137,500 ha. We found that LFS were frequently observed across a relatively large portion of their range, including East San Pablo Bay north into Suisun Marsh down through Grizzly Bay and all four regions of Suisun Bay through the Confluence to the Lower Sacramento River region. Unlike juvenile LFS, whose locations fluctuate between the bays and Suisun Marsh in relation to the low salinity zone, adults during the spawning period appeared to be not only in these locations but also in upper Delta reaches and also into San Francisco Bay, likely indicating that LFS spawning habitat may extend further upstream and downstream than LFS rearing habitat. The anadromous life stage declined in spring and mid-summer but increased throughout fall months across all areas, suggesting immigration and emigration through the Estuary. Longfin smelt appeared to migrate completely out of the lower rivers by July but some adults consistently remained in downstream Estuary areas, suggesting not all individuals demonstrate marine migration. This comprehensive data review provides managers and scientists an improved depiction of the spatial and temporal extent of LFS throughout its range within the Estuary and lends itself to future population analysis and restoration planning for this species.