Abstract. Abstract Aim: We assessed the effect of environmental factors on the structure of periphytic ostracods communities along the river-floodplain system of the Upper Paraná River. We predict that the higher distance from Porto Primavera dam downstream would lead to higher diversity and density of the ostracods. Methods Periphytic ostracods (associated with root systems of the floating Eichhornia spp) were sampled during November 2013 to May 2015. Three samples were collected at each sampling site (channel of the Paraná River, tributaries and lakes). Eichhornia plants were removed from the water by hand and the plants were placed in a plastic bucket. Roots were washed for the removal of ostracods, and samples were filtered through a hand net with 160 µm mesh size. Results The faunistic survey recorded 44 ostracods species and richness estimators indicated that sampling effort appears to be suitable to reveal the diversity of ostracods in this studied area. The highest richness and density were observed in the stretch downstream of the dam in the main channel of Paraná River and in the lakes. Beta diversity was not significantly different along the longitudinal gradient downstream and higher similarity of ostracods species composition was observed in the lakes located in the stretch downstream of the dam. Conclusions An increase in the richness and density of ostracods were recorded in the sections downstream of the Paraná River, evidencing the importance of undammed tributaries on the ostracods community. The similarity of beta diversity amongst sampling sites may be owing to permanent hydrological connectivity amongst these environments, favouring the exchange of organisms mainly through the drift of free-floating macrophytes, and owing to the passive dispersal of drought resistant eggs of ostracods. Local abiotic factors had significant effects on abundance and distribution of some ostracod species.