The aim of this study was to analyze the density, diversity, biomass and assemblage composition of the phytoplankton in relation to environmental conditions (physical, chemical, hydrological and meteorological variables), measured under the different scenarios caused by the ENSO phenomenon in the period between 2005 and 2012, in six sampling sites in the tidal freshwater zone of the Río de la Plata estuary, covering almost 100 km of coastline. The results revealed changes in the structure of the phytoplankton, such as a significant reduction of diversity, and decreases in biomass and phytoplankton density, particularly during El Niño phases. Cyanobacteria were more abundant in the neutral periods, Chlorophyceae dominated La Niña phase while Bacyllariophyceae dominated El Niño. However, no complete replacement of species between cycles was observed. The results obtained were highly variable due to the inherent natural variability of the Río de la Plata, emphasized by the anthropogenic impact in this area.Instituto de Limnología "Dr. Raúl A. Ringuelet"