Previous studies have demonstrated that macro-scale climatic events such as ENSO, cause changes in meteorological and hydrological conditions, inducing physicochemical changes in the water column, as well as in coastal and estuarine communities in the Atlantic Ocean. Rio de la Plata (RdlP) is the second largest estuary of South America, where ENSO is a macro-scale environmental driving force. In this paper, the species composition, abundance, as well as the temporal and horizontal variation of the mesozooplankton in the north coast of the RdlP during 2009-2010 ENSO were analyzed. Zooplankton samples were collected with sub-surface trawls in fifteen stations during eleven sampling surveys. Physico-chemical parameters of the water column (temperature, salinity, dissolved oxygen, turbidity, and chlorophyll a) were determined and related to the RdlP flows. The holoplankton was dominated by estuarine copepod (Acartia tonsa), freshwater cladocerans (Bosmina hagmanni, Ceriodaphnia dubia, Moina sp.), and in the meroplankton, barnacle larvae were the most abundant group. Temporal variability was reflected in abundance differences and ecological indexes between both ENSO phases. The copepods abundance showed a positive association with RdlP flow during El Niño (Nov 2009-Apr 2010), and negative during La Niña-Neutral (Sep 2010-Jan 2011). During El Niño months, the higher richness of typical freshwater cladocerans was observed, promoting a horizontal heterogeneity in the study area. During La Niña-Neutral, the zooplankton showed lower species richness and was dominated by copepods typical of the RdlP (Acartia tonsa). Canonical Correspondence Analysis showed that salinity, RdlP flow, and chlorophyll a explained 88.4% of the total variance of the species-environment relationships. This paper presents new information on zooplanktonic organisms’ response to climatic and hydrological events in the RdlP estuary.