In this work, spatial and temporal variations in the diversity (species richness and Simpson's Diversity Index) and abundance (indexed by the capture per unit effort--CPUE; total and for reproductive groups) of fish from three rivers (Baía, Ivinheima and Paraná) located in a floodplain of the Upper Paraná River basin were analyzed over a period of 20 years (1987-2007). In addition, we evaluated the relationships of these ecological attributes with variations in the hydrologic regime, considering the possible effects of natural (climatic events) and artificial (discharge control by dams) disturbances. Annual variations in hydrometric attributes were calculated using PULSO software and daily water level data. We applied analysis of covariance to determine the relationships between ecological and hydrometric attributes, the latter summarized in axes of a principal component analysis. Lower values of the fish assemblage attributes (diversity and abundance) were registered in the Paraná River. Species richness, total CPUE and CPUE of long-distance migratory species were positively related to the duration of the floods and the connectivity of the area. Variations in the annual hydrological cycle and their effects on fish assemblage appear to be affected by extreme natural (ENSO) and artificial (discharge control by dams) events.