Data are presented on the quantitative relations between water chemistry and phytoplankton productivity in San Francisco Bay between March 1976 and July 1977. Spatial distributions are listed for: salinity, temperature, transmission, chlorophyll-a, fluorescence, dissolved oxygen, orthophosphate, nitrate + nitrite, nitrite, ammonia, particulate organic carbon, alkalinity, pH, pCO2, suspended sediment and turbidity. These samples were collected at 36 stations located along the axis of the Bay from Rio Vista on the Sacramento River to Calaveras Point in South San Francisco Bay, and along transects from the Golden Gate Bridge to the Farallon Islands. Also reported are the results of 59 experiments measuring in situ rates of micronutrient uptake and phytoplankton productivity at 9 locations throughout the Bay.