This study was developed in different environments of the Ivinhema river floodplain in order to analyze the spatial and temporal variation of benthic assemblages and their relationship with physical and chemical variables and water level. Samples were taken quarterly between February and November 2002 in four environments: Ivinhema main channel, Ipoitã channel, Patos lake (with direct connectivity) and Ventura lake (without connectivity). The system was characterized by a bimodal potamophase cycle with moderate intensities and large amplitudes, remaining in potamophase for 184 days in 2001 and 67 days in 2002. Physical and chemical parameters, summarized in a PCA, showed spatial and temporal variation. Moderate intensity and great width pulses were recorded. Physicochemical variables changed spatially and temporally. Nematoda, Corbiculidae, Oligochaeta, Acari, Ostracoda and Chironomidae were the most abundant taxa registered and the larvae of Chironomidae were the most predominant in the Ivinhema main channel, Ipoitã channel and Ventura lake. Total density changed between months, but the analysis of the structure of the assembly (CA) showed that the benthic assembly of the Ivinhema main channel is dissimilar to the ponds. The relationship between PCA and CA was not significant, indicating that the Ivinhema system had a complex structure and that the spatial uniformity of density and temporal uniformity of benthic assemblage is due to the greater connectivity between the sites.