An examination of factors influencing fish assemblages in the tidal freshwaters of the San Francisco estuary

The tidal freshwater Sacramento-San Joaquin Delta (hereafter Delta), located at the eastern boundary of the San Francisco Estuary, is considered one of the most damaged ecosystems in the world. In recent years, native fish diversity and abundances have declined dramatically. Managers and scientists are attempting to restore native fish populations but many of the mechanisms underlying their responses to changes in habitat and riverine inflows remain outstanding. In Chapter 1, I investigated the salvage patterns of fishes between 1992 and 2005 at two of the largest water diversions in the world, the State Water Project and Central Valley Project. I found that the direction and magnitude of flows through the estuary and to the export facilities were reasonable predictors of pelagic fish entrainment. In Chapter 2, I investigated the abundances and diets of ichthyoplankton in the south and north Delta between 2005 and 2007 to determine the diel and spatial distributions of certain species over the course of two consecutive tidal cycles. I found that larvae of pelagic species exhibited diel shifts in abundance and feeding incidences whereas other larvae aggregated in littoral samples with less obvious diel behaviors. In Chapter 3, I examined the spatial and temporal distributions of fishes at a reference and three restored marshes in the Delta between April 1998 and July 1999. Fish assemblages were most distinguishable by species that aggregated in and around submerged aquatic vegetation (SAV) versus species found in open-water (offshore and nearshore) or tidal slough habitats. Overall, my findings support conclusions drawn previously; physical modifications and biological introductions have had irreversible and significant impacts to native fishes and their habitats. Nonetheless, my research suggests that entrainment of some native species can be effectively reduced by manipulating system hydrodynamics or by timing diversions during periods when they are less vulnerable to entrainment. To maximize potential benefits to native fishes, restoration efforts should focus on recreating habitats that will minimize colonization of SAV.