Chinook smolts tend to migrate through San Pablo and Central Bays in a few days’ time (Hearn et al. 2010, Jahn 2011a, Hearn et al. 2013). The fish also tend not to enter South Bay, and are not taken in significant numbers south of Hunters Point (Jahn 2011a). Because of their low abundance in South Bay and their tendency to remain in deep water while emigrating from their rearing habitats, it is very unlikely that any of the listed chinook ESUs will enter Brisbane Lagoon.

The only likely occurrence of the species at the project site is spawning sites in the South Bay and during out-migrations of anadromous juveniles heading from freshwater to ocean habitat. Although the great majority of outmigrating juveniles never enter South Bay, it It is possible that individuals of this these species could occasionally enter Brisbane Lagoon via the box culvert that connects the Project Site with the Bay. tTherefore, the analysis in this section is based on presumed occurrence. Smolts and juveniles would not be prevented from entering the Project Site as part of their known behavior to remain in estuarine habitats before migrating to the ocean.

Longfin Smelt (Spirinchus thaleichthys) California Threatened. The life history and distribution of longfin smelt in the San Francisco Estuary are best described in a recent paper by Merz and others (2013). These authors characterize the species as estuarine, but with many individuals undergoing a migration to the ocean for several months. The species exhibits a 2-year life cycle and spawns in the low salinity zone and fresh water of the Delta in winter and early spring. The larvae gradually spread into the lower bays in spring and summer as they transform into juveniles.

A well-documented decline in numbers of this species (Rosenfield and Baxter 2007) occurred in about 2001 and is the reason for the State listing. From 2001 to 2011, the average otter trawl catch of longfin smelt in South San Francisco Bay stations nearest the Project site has been about one fish per hectare (Table 4.C-2); data courtesy of CDFW's San Francisco Bay Study and the Interagency Ecological Program for the San Francisco Estuary). The catch rate is somewhat less than abundance per se, because of inefficiencies in the sampling gear. However, longfin smelt are an open water species and would be expected to be even less abundant near shore, where the CDFW trawling vessel could not venture. This expectation is borne out by the CDFW beach seine program, which ran from 1980 to 1986 and consisted of monthly sampling at eight South Bay Stations (Orsi 1999). This effort yielded only 7 specimens of longfin smelt, at a time when longfin smelt were approximately six times as abundant in South Bay as they are now (Table 4.C-3).