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The main environmental problem in urban areas, especially in Brazil, is the discharge of untreated sewage. The in vivo Drosophila melanogaster Somatic Mutation and Recombination Test (SMART) was used to assess the genotoxicity of surface waters from three different sites in the Tocantins River, Brazil. The in silico approach was used to search for known and predicted interactions between environmental chemicals found in our samples and Drosophil a and human proteins. The genotoxicity tests were performed in standard (ST) and high bioactivation (HB) crosses with samples collected at two periods, the rainy and dry seasons. Mutant spot frequencies found in treatments with unprocessed water from the test sites were compared with the frequencies observed in negative controls. The collection points were represented as sites A, B and C along Tocantins River. Sites A and B are located in Porto Nacional City, whereas site C is located in Palmas City. Considering the rainy season collection, positive responses in the ST cross were observed for sites A and C (89.47% and 85% of recombination, respectively) and in the HB cross for sites A, B and C (88.24%, 84.21% and 82.35% of recombination, respectively). The positive results in the dry season were restricted to sites A and B (88.89% and 85.71% of recombination, respectively) in the HB cross. In accordance with in vivo and in silico results, we hypothesize that ribosomal proteins (RPs) in fruit fly and humans are depleted in cells exposed to heavy metal causing DNA damage and chromosome instability, increasing homologous recombination.