The El Niño phenomenon refers to a warming of the tropical Pacific basin whose meteorological effects influence the dynamics of aquatic ecosystems around the world. Prior studies have shown that strong El Niño events are highly correlated with high rainfall episodes and high freshwater discharge into subtropical estuaries, with subsequent changes in species composition, abundance, and diversity of their biota. In this work, we evaluated the hypothesis that riverine allochthonous matter associated with the strong 2015 El Niño event is assimilated by decapod crustaceans and fishes of a southwestern Atlantic estuary. We analyzed carbon (δ13C) and nitrogen (δ15N) stable isotope ratios of primary food sources and consumers in the estuary and of riverine allochthonous matter. Our findings revealed that higher water surplus and lower salinity associated with the 2015 El Niño coincided with an increase in the number of freshwater fish species and a decrease in the number of marine- and estuarine-dependent fishes inside the estuary. In addition, most estuarine consumers had lower average δ13C values during the wet period associated with the 2015 El Niño. This seemed to reflect the assimilation of 13C-depleted riverine matter, which according to Bayesian isotope mixing models ranged from 11% (adult resident decapod crustaceans) to 60% (adult resident fishes) during the wet season. Further studies are needed to evaluate the role of El Niño events on structuring food web organization in estuaries under the influence of this climatic phenomenon, which may become more frequent and intense in a global warming scenario.