Benthic microalgae biomass (chlorophyll a) data from San Francisco Bay are presented for the period February 1980 through February 1981. Benthic chlorophyll a was sampled throughout the bay (maximum of 54 stations) at bimonthly intervals and at monthly intervals at up to 14 stations in the southern bay. Ancillary data collected concurrently with the benthic chlorophyll a data include sediment phaeopigment concentration and grain size; and water column salinity, temperature, chlorophyll a (in vivo fluorescence), and extinction coefficient.