Exposure to certain pollutants induces a series of alterations in deoxyribonucleic acid (DNA) that may result in genotoxic/mutagenic effects in exposed individuals. The present study aimed to monitor genotoxic, mutagenic, and recombinogenic potential and consequently water quality in two streams in the Paranaíba River basin in the state of Minas Gerais, Brazil, using two bioindicator fish (Rhamdia quelen and Geophagus brasiliensis). The micronucleus (MN) test and somatic recombination and mutation test (SMART) were employed to assess DNA damage. The water quality index (WQI) at the reference site control (S1) due to its proximity to the river source was compared to Córrego do Óleo (S2) with respect to chemical parameter levels of biochemical oxygen demand (BOD), dissolved-oxygen rates (DO), and total solid and fecal coliform counts. These chemical parameters were above the permitted limits at Córrego do Óleo (S2). At a third site, Córrego Liso (S3), a poor WQI was detected, attributed to the influence of domestic and industrial activities where BOD, DO, total solid, fecal coliform, total phosphorus, and turbidity rates exceeded premissible limits. The MN frequencies and the numbers of MN per cell (CMN) at sites S2 and S3 were significantly higher than those at S1 in both species. It is of interest that the increased frequency of MN was similar to the positive control cyclophosphamide only at S3, suggesting that the effects of water contaminants were most severe at this site. At sites assessed (S2 and S3), there was a significant rise in somatic mutation and recombination in the wings of Drosophila melanogaster, indicating the presence of trace elements, mainly lead (Pb) and cadmium (Cd), in the effluents in the Paranaíba River basin sites.