Pollution of water resources by toxic urban, industrial and agrochemical pollutants is a growing problem all around the world. In a river shared between two countries, such as the Rio Uruguay (geographical limit between Uruguay and Argentina), the problem seems to be worse. We used the micronuclei assay (MN) to evaluate the exposure of Salminus brasiliensis and Leporinus obtusidens to genotoxic agents in the lower regions of this river. S. brasiliensis showed higher percentages of micronuclei with respect to L. obtusidens, probably due to bioaccumulation. However, both species exhibit a chronic exposure to genotoxic agents according to the MN test.