In southern Brazil, cold (La Niña) and warm (El Niño) episodes of the El Niño Southern Oscillation (ENSO) phenomenon cause drought and high rainfall, respectively. The low precipitation and freshwater outflow associated with La Niña during 1995–1996 were associated with an increase in the abundance of marine species in the Patos Lagoon estuary. During the 1997–1998 El Niño, high precipitation and river discharge were associated with low abundance of marine species in the estuary. ANOVA results showed a higher abundance during La Niña than El Niño for estuarine resident (RES) and estuarine dependent (DEP) fishes. During La Niña catch per unit of effort (CPUE) of RES increased from the marine to estuarine area, but during El Niño CPUE increased at the marine area and diminished during summer and autumn in some estuarine sites. DEP fishes had an opposite abundance pattern. During La Niña, these fishes were abundant at the coastal marine area and along some estuarine sites, but during El Niño, CPUE remained almost the same at the marine area but dropped along some estuarine sites. These different abundance patterns for dominant fish groups yielded a positive interaction between stations and climatic events. With higher river discharge and the consequent decline of dominant euryhaline fishes, such as Mugil platanus and Atherinella brasiliensis, freshwater species increased in abundance and richness in the shallow waters of the stuary. The ENSO phenomenon influences precipitation and estuarine salinity in southern Brazil and thereby seems to have a strong influence on recruitment, immigration, and emigration dynamics of fish species living within and adjacent to estuarine habitats.