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This Data Release makes available measurements of phytoplankton species composition, abundance and cell size made on samples collected in San Francisco Bay (CA) from January 2014 through December 2018. Whole water phytoplankton samples were collected at least monthly at fixed sampling stations along a 145-km transect where the variability of salinity, temperature, turbidity and nutrient concentrations reflected a broad range of environmental factors that regulate phytoplankton growth and abundance. A map and table of sampling locations are included in this Data Release. Immediately after samples were collected, they were preserved with acid Lugol’s solution. The samples were analyzed by BSA Environmental Services,...