ABSTRACT ENSO phases produce changes in precipitation and river flow in Eastern South America. We aimed to evaluate phytoplankton and surface sediment diatoms' response to ENSO within the Río de la Plata estuary. A 180-km-long transect off the Uruguayan coast was undertaken in May 2009 (La Niña) and May 2010 (El Niño), where physical, chemical and biological variables were measured. During El Niño we registered lower temperatures/salinities throughout the transect, and the riverine zone was specifically more homogeneous in terms of temperature, salinity, turbidity and chlorophyll-a than during La Niña. We observed changes in the species composition of both planktonic and sediment diatoms. Concomitantly, a significant depletion in planktonic diatom abundance and richness in both planktonic and benthic domain during El Niño was observed. In addition, there was a higher proportion of dinoflagellates than during La Niña, which was explained by a higher water column stability. The dominance of the chain-forming and meso-eutrophic diatom Aulacoseira was registered during El Niño in both domains, mainly in the fluvial zone, related to a high river discharge. Our findings are important to anticipate changes in microalgae composition related to oceanographic variability during potential ENSO events.