The Asian freshwater invasive bivalve, Limnoperna fortunei (Dunker 1857), was introduced into South America through the Rio de la Plata estuary (Argentina) at the beginning of the 1990s. Between 1995 and 1996, the bivalve was first observed in the middle reaches of Paraná River, 600 km upstream from its original point of entry to the system. Here, we describe the present zooplankton communities of two secondary channels of the Middle Paraná River floodplain (Colastiné and Santa Fe rivers) and contrast them with pre-invasion communities using zooplankton data obtained during 1974–1975 (Sante Fe River) and 1971–1973/1981–1982 (Colastiné River). In both floodplain rivers, total zooplankton and rotifer abundance during low water were significantly lower in the post-invasion period than they were pre-invasion. Prior to invasion, mean zooplankton abundance in low water was greater than in high water, while post-invasion mean zooplankton abundances during low and high water were similar. The rotifer Keratella was significantly more abundant prior to mollusc invasion. Zooplankton abundance and chlorophyll-a concentration declined compared to the pre-invasion period and were not correlated with post-invasion physical factors. Nutrient concentrations increased post-invasion from increased human development, but did not stimulated zooplankton or phytoplankton.