Seasonal variations in the composition and carbon biomass of diatoms and other phytoplankton groups were analyzed over two years, from December 1996 to January 1999, at a fixed station in Anegada Bay, within the El Rincón estuarine system (38–41°S). Phytoplankton communities characterizing the different seasons were identified by classification and detrended correspondence analyses. Diatom communities were highly speciose, with 117 species recorded during the two-year study. Three diatom species are new records for the Argentinean Sea (i.e., Minidiscus trioculatus (F.J.R. Taylor) Hasle, M. decoratus Chrétiennot-Dinet & Quiroga and Thalassiosira tealata Takano). Phytoplankton taxonomic composition and carbon biomass showed a strong seasonality, with two carbon (C) biomass maxima occurring in summer and winter (maximum concentration: 193 μ g C L−1). Summer blooms were mainly dominated by tychoplanktonic diatom species (Paralia sulcata (Ehrenberg) Cleve, Rhaphoneis amphiceros (Ehrenberg) Ehrenberg and Delphineis surirella (Ehrenberg) Andrews), probably resuspended from the sediments, and by the pelagic diatom T. hendeyi Hasle & Fryxell. The winter phytoplankton community was characterized by a high number of diatom species and a high carbon biomass of diatom resting spores. The occurrence of the winter bloom seems to be closely associated with the inoculation of the water column by diatom resting spores. Maximum diatom carbon biomass corresponded to periods of increased freshwater inflow, whereas seasonal variations in diatom taxonomic composition may be explained by the life-cycle strategies of the species. The taxonomic composition and temporal succession of phytoplankton communities in Anegada Bay are comparable with previous studies in Blanca Bay, suggesting relatively uniform phytoplankton seasonality over shoals in the El Rincón estuarine system.