Most changes in water bodies are result of human activities that have the potential to undermine the environmental integrity of aquatic ecosystems. Changes in genetic material can be evidenced by the frequency of nuclear abnormalities in fish blood cells, in response to genotoxic agents even at low concentrations. Thus, we aimed at comparing the frequencies of nuclear abnormalities of fish kept in acclimation, with fish collected in Timbo river (Santa Cruz do Timbo, Santa Catarina State), under low anthropogenic interference, and fish collected in Iguacu river (Uniao da Vitoria, Parana State), a polluted river. The highest frequency of changes in nuclear morphology of fish erythrocytes was found in the urbanized area around the Iguacu river, while, the fish collected in areas with preserved riparian forest surrounding the Timbo river and acclimated fish showed no morphological changes. Our results suggest that genotoxic compounds in the Iguacu river are acting as stressors to aquatic communities, especially fish. In addition, the absence of nuclear abnormalities in fish from the Timbo river suggests that rivers without significant environmental changes can serve as reference point for comparative studies of genetic modifications for the species studied.