We investigated the occurrence and seasonal variation of the biomass of rotifers, tintinnids, the heterotrophic dinoflagellate Gyrodinium fusus and copepod nauplii in the Bahía Blanca Estuary (38°42′S61°50 ′W), Argentina, during an annual cycle. The rotifers fauna comprised three species, while the tintinnids were represented by sixteen species. The biomass of the rotifers fluctuated between 0.62 and 8.90 µgC l−1. The biomass of the tintinnids fluctuated between 0.13 and 9.37 µgC l−1, the biomass of the nauplii stages between 1.78 and 7.65 µgC l−1; while the biomass of G. fusus varied from 0.26 and 7.94 µgC l−1, these results are compared to estimates of microzooplankton in other regions. We analysed the presence of the different groups in relation to the environmental variables, based on point-biserial correlation. Salinity fluctuated between 25.14 and 36.64; temperature between 7.5 and 23.2°C, solar radiation between 0.9 and 30.8 MJ m−2d−1 and Secchi distance between 0.25 and 1.43 m. Rotifers were correlated positively with temperature, chlorophyll-a and Secchi depth and negatively with salinity. The tintinnids were positively correlated with salinity. Gyrodinium fusus was positively correlated with Secchi depth, and chlorophyll-a, and negatively with temperature and solar radiation. Nauplii stages were negatively correlated with chlorophyll-a. Based on the occurrence of the microzooplankters in relation to the physico-chemical variables, it was possible to establish two seasonal assemblages: (a) the co-occurrence of the rotifers and the heterotrophic dinoflagellate G. fusus during the winter–spring; and (b) the tintinnids and nauplii larvae during the summer. We conclude that, in this estuary, physico-chemical variables are the forcing factors that directly, or indirectly, influence the seasonal assemblages of the microzooplankton.