streams, where they die after spawning. Chinook appear to make little use of near shore habitats in San Francisco Bay (as opposed to the brackish marshes upstream of San Pablo Bay; Williams 2006). This is because the fish (at least in modern times) migrate rapidly through the lower bays on their way to the ocean (MacFarlane and Norton 2002, Hearn et al. 2010, Jahn 2011a, Hearn et al. 2013). In the CDFW Bay study, trawl captures of juvenile chinook of all sizes/stages (fry/fingerling/smolt) were mainly in the deep channels of San Pablo and Central Bay (Jahn 2011a). Chinook considered by CDFW not to be fall-run fish (i.e., the larger fish believed to represent winter-, spring-, and late fall-run ESUs) were taken in CDFW's Bay study mainly in the months of April through early June (Jahn 2011a), although the size-at-date criteria by which the fish were assigned to runs are not reliable (Williams 2006, Jahn 2011b).

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