This study is an evaluation of the mutagenic and cytotoxic activity of sediments in Bom Jardim stream, one of the tributaries of the Cai River basin, Rio Grande do Sul, Brazil. This stream receives an indirect contribution of treated effluent from a petrochemical plant. The Salmonella/microsome assay, a microsuspension method, was used to evaluate moderately polar extracts of sediment samples at three points along the stream. The grain size analysis showed a lower mean content of fine particles in the principle face (front) of the complex, and this was also the sampling point with the lowest percentage of extracted organics. Low mutagenic activity was observed at the different sites studied, ranging from 3.3 to 8.3%; cytotoxic activity was more important in this area, ranging from 20 to 40%, adding up the results of assays in the presence and absence of external metabolism. In assays without S9mix there were more frequent mutagenic and cytotoxic responses, with frameshift mutations being the most frequent. The results also showed that there was a gradual, seasonal distribution of the responses as the stream mouth is reached, the most compromised points being in front of and downstream of the complex. Mutagenic and cytotoxic activity in sediment samples has proved important to determine environmental quality, despite the complexity of the chemical composition of the environmental matrix. Furthermore, use of the Salmonella assay to monitor mutagenesis and cytotoxicity helped identify the presence of pollutants. This assay is an important tool, aimed mainly at actions to preserve the genetic heritage of the fauna and flora affected by human activity and to improve environmental quality.