The U.S. Geological Survey conducted hydrologic investigations in San Francisco Bay between January and November of 1995. 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 the channel portions of both northern and southern reaches of the bay, and at shallow water stations in the southern reach. This report presents the sampling and analytical methods and the data from these studies. Measured salinity values for the nutrient samples are also reported. Data on the variability due to sampling and sample handling procedures, and on the precision of the analytical methods are also presented.