We studied the changes in geochemical variables in the middle section of Río de la Plata estuary during the 2009–2010 El Niño–Southern Oscillation (ENSO) event. Protein, organic matter, chlorophyll-a and phaeopigment content of surface sediments were significantly correlated with the increased continental freshwater input associated with high total monthly rainfall. During the warm-phase ENSO event, river flow was 5-fold larger than average historical levels, which led to a steady decrease in salinity values and the highest levels of geochemical variables. The evidence presented herein suggests that warm-phase ENSO events increase the trophic state of the sediments because of the increased freshwater input. Thus, our findings may be useful to anticipate potential eutrophication episodes in the study area.