The U.S. Geological Survey conducted hydrologic investigations in San Francisco Bay during Water Years 1988, 1989, 1990 and 1991. Dissolved inorganic plant nutrients, nitrate, nitrite, ammonium, silica, and reactive phosphorus were measured in surface and in near-bottom waters at previously established locations in both northern and southern reaches of the bay. Salinity, turbidity, and concentrations of suspended particulate matter also were measured. Additionally, in Water Year 1991, concentrations of dissolved organic nitrogen and phosphorus were measured. From November 1990 through April 1991, surface waters were sampled near the end of the old Dumbarton Bridge (east span). Salinity, dissolved inorganic nutrients, and alkalinity were measured for these samples. This report presents the sampling and analytical methods, and the data for these studies.