This study characterizes the likely interaction of surface water and sediment samples with DNA to quantitatively and qualitatively establish their mutagenic and/or recombinagenic activity. Samples were collected at 5 different sites within the area of Araçá Stream and 2 different sites within the Sinos River mouth and Garças Stream in the municipality of Canoas, RS, Brazil. The area is impacted by untreated urban discharges (sites 1-7), agricultural pesticides (sites 5 and 7), hospital waste (site 3), animal dejects (site 5), small industries (sites 4, 5 and 6) and vehicular discharges (sites 2, 4, 5 and 6). The wing Somatic Mutation and Recombination Test (SMART) in Drosophila melanogaster was used. The test detects simultaneously mutations and recombination induced by the activity of genotoxins of direct and indirect action. All the samples displayed a massive recombinagenic response, but no mutagenic activity was detected in any of the evaluated samples. This study was done in D. melanogaster with unprocessed water and sediment samples attributing a massive and exclusive recombinagenic action associated to the induction of homologous recombination--a genetic phenomenon involved in the loss of heterozygosity.