Aquatic monitoring is an important tool for identifying potential compounds in rivers that may damage the environment. Here, we evaluate the potential genotoxic effects of water samples from São Francisco River (Brazil) using the micronuclei (MN) assay in resident species, Astyanax paranae. Four seasonal collections occurred between the years 2009 and 2010, at three locations between two nearby cities in the region. It was clearly observed an increase of MN frequency in fish caught in the river. This result is most likely due to the sewage contamination from the treatment plant, the waste pesticides from crops and the lack of riparian vegetation along the river, especially during the winter when there was a significant increase in the frequencies of MN. These results indicate that compounds in waters from São Francisco River may have genotoxic effects and consequently, cause damage to the environment as well as to human health.