Physico-chemical and toxicological analyses are of fundamental importance to determine water quality. The objectives of the present study were to evaluate the toxicity, mutagenicity and carcinogenicity of samples from the Mumbuca Stream and the Perdizes River, through both SMART and the wts test, respectively, in somatic cells of Drosophila melanogaster and to quantify the amount of heavy metals and other pollutants, which are indicative of environmental quality. Water samples were collected (M1, M2, P1, P2 and MP) and submitted to physico-chemical analysis, calculating the water quality index for each sampling site. In order to evaluate the toxicity, mutagenicity and carcinogenicity of the samples, third instar larvae descended from the crossing between virgin female wts/TM3, sb and mwh/mwh males (wts test) and ST and HB (SMART) crosses were treated with samples from P1, P2, M1, M2 and MP sites. The physico-chemical analysis and the biological assay allowed us to conclude that undetected values for heavy metals and the low frequency of mutant spots (SMART) and epithelial tumor (wts) in treated flies from the Mumbuca Stream and Perdizes River may be due to the reduction of ceramic activities in the municipality. The physico-chemical analyzes identified altered the environmental quality parameters, which directly influenced the survival of D. melanogaster treated with samples of M2 and MP, which according to the WQI were classified as regular and poor environmental quality, respectively. The altered parameters may be due to clandestine domestic sewage sent downstream of the effluent.