Numerous pollution factors generate changes in water quality and in organisms that depend on this resource, as they may contain substances with mutagenic, genotoxic and cytotoxic properties that affect the genetic integrity of organisms. The Clarimundo Stream is located in the city of Cerro Largo, Rio Grande do Sul, Brazil, from which it passes through an agricultural area and crosses the city receiving discharges of untreated household waste. This work evaluated the genotoxic potential of these waters through a bioassay with Allium cepa, usually used in biomonitoring studies. Four water collections were conducted in each season and three points were marked for the analyses. The Allium cepa bulbs were germinated for 72 hours, in the proportion of three for each sample of collection points and three in distilled water for control parameters. Subsequently, the roots were submitted to the Feulgen procedure with modifications, for the preparation of the slides. The data were submitted to statistical analysis by the Tukey test with reliability of 5%. The results showed chromosomal alterations and Mitotic Index values suggesting that the water of Clarimundo Stream has the potential to cause damage to the genome of eukaryotic organisms.