Historically, aquatic ecosystem restoration has attempted to return a region to past or pristine conditions, which is often unachievable. Here I examine a different approach using a target fish community analysis that efficiently reveals aspects of the ecosystem that are most important for site improvement. The target community is comprised of the relative proportions of fish species that should be at a location based on fish present in biologically similar reference sites considered to be ecologically acceptable. Comparison with the current proportions of species at the restoration site reveals specific objectives on which ecologists can focus in order to maximize restoration efforts. This study examines the effectiveness of target fish community analysis in the San Francisco Bay, the largest estuary on the Pacific coast, using four coastal estuaries: Columbia Estuary, WA/OR; Tillamook Bay, OR; Morro Bay, CA; and Santa Monica Bay, CA. Trawl data from South San Francisco Bay conducted by the Marine Science Institute in Redwood City, CA from 1970 - present were used for the comparison. Data revealed no changes in species abundances through time, and benthic species were consistently underrepresented relative to the target. In addition, pelagic Northern Anchovy were overabundant even though they were the most prevalent species in the target. I propose that the dominant Northern Anchovy benefits from eutrophic conditions and increasing food availability, which lowers benthic oxygen and results in lower fish abundance. In addition, toxins such as mercury and polychlorinated bisphenols buried in sediment could contribute to low abundances of benthic species. The study showed that restoration efforts should focus on eutrophication and sediment toxicity as important aspects of the San Francisco Bay that impact fish communities and that the target community analysis has great potential for systems with appropriate reference sites.