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, Inc following the McNabb (1960) filter method. Following standard methods, at least 400 natural units (colonies, filaments, and unicells) were enumerated to the lowest possible taxonomic level from each sample. In 2014 and 2015, abundances were estimated by random field counts with at least 100 cells of the most numerous taxon counted. From 2016 onward, the 400 natural unit tally was met using two separate random field count efforts: (1) at least 100 natural units of organisms smaller than or equal to 5 μm were identified and enumerated; and (2) at least 300 natural units of organisms larger than 5 μm were identified and enumerated. The 2016 method was adopted to maximize detection of large but rare cells. For all data, cell volumes for each taxon were estimated with the formulas for solid geometric shapes that most closely matched the cell shape according to Hillebrand et al. (1999). Cell volume calculations were based on measurements of up to ten organisms for the most abundant taxa. The Biovolume (cubic microns per ml) of each taxon was computed as the product of abundance (cells per ml) and cell volume (cubic microns per cell). In order to assess replication of results, 10 duplicate samples were collected and analyzed in 2017 and are reported here. Hillebrand, H., Dürselen, C.-D., Kirschtel, D., Pollingher, U. and Zohary, T. 1999. Biovolume Calculation for Pelagic and Benthic
Microalgae. Journal of Phycology, 35: 403–424. doi:10.1046/j.1529-8817.1999.3520403.x McNabb, C. D. 1960. Enumeration of freshwater phytoplankton concentrated on the membrane filter. Limnol. Oceanog., 5: 57-61.