The San Francisco Bay Study was established in 1980 to determine the effects of freshwater outflow on the abundance and distribution of fish and mobile crustaceans in the San Francisco Estuary, mainly downstream of the Sacramento-San Joaquin Delta. The Bay Study survey currently samples open-water stations from a research vessel with two types of trawl gear: a midwater trawl to sample the pelagic community, and an otter trawl to sample demersal organisms. Historically, the study also included plankton sampling (1980-1989). In both otter and midwater trawl samples, fish, crabs, and gelatinous zooplankton are identified to species, and length/size data are collected on a representative subsample. Shrimp species are collected from each otter trawl sample and biometric data are collected in the lab (counts, sex, gravid-status, length). Several physical and water quality parameters (temperature, salinity, conductivity, water clarity and depth) are collected at each station to describe estuarine environmental conditions that relate to abundance and distribution trends. This publication will include fish and water quality data. Some metadata are included for crab, shrimp, and gelatinous zooplankton and publication of this data will follow.