In crop farms, it is common to use animal livestock manure as soil biofertilizer, as well as agricultural defensives that can reach to ground and surface waters. Waterborne microorganisms as Salmonella and Escherichia coli can cause gastroenteritis to consumers, and the presence of chemical compounds can cause DNA mutation damages in exposed organisms. Thus, the present study aimed at quantifying E. coli and Salmonella in surface water from the Suruvi river (located above the Guarani aquifer) and evaluating the water genotoxic potential using Allium cepa as a model. For that, five sampling sites were established, and water samples were collected from March/ 2013 to June/2014, and submitted to bacteria enumeration, and genotoxicity assay. Moreover, rainfall volume and air temperature were measured. Results indicated the occurrence of Salmonella in 14 % of the samples and high amounts of E. coli ([1875 MPN/100 mL). The amount of E. coli decreased as the rainfall volume increased. The genotoxicity assay results showed that water contains substances, which are able to induce changes in mitotic index on the root meristem cells of A. cepa. In summary, surface water sources are contaminated with fecal material and genotoxic substances, emphasizing the importance of surveillance of surface and groundwater in this region, especially because of the proximity to the Guarani aquifer.