An approach was developed to evaluate ecotoxicological effects in river basins impacted by anthropic industrial discharges. Genotoxicity was the first level of evaluation of the river water, but when cytotoxicity was associated with genotoxic effects, our research group added chronic assays allowing the assessment of the ontogenic cycle in environmental diagnosis. The genotoxicity of river water sampled during two periods was compared using the microscreen phage-induction and Salmonella/microsome assays. The study assessed the ability of these assays to diagnose environmental quality in an area where petrochemical impacts occur. The study was performed at six sampling sites using the Salmonella/microsome assay for 10 sampling periods and the microscreen phage-induction assay for 15 samplings. The percentage of mutagenic activity was higher at the sites sampled in front of the petrochemical complex in both periods, but there were more significant mutagenic responses in the first assessment. However, comparing the percentages of samples with mutagenic and cytotoxic activity observed during the two periods it becomes clear that there are more cytotoxic samples during the second period throughout the area studied. The genotoxic activity analyzed by the microscreen phage-induction assay was constant in the second period. Chronic toxicity studies with the microcrustacean Daphnia magna confirm the toxic effects observed. The mortality of individuals was higher at the site most influenced by the petrochemical complex, followed by the station located upstream from this area, while the formation of ephippial eggs was uniform at all stations. The rise in the toxic potential of the region detected by cytotoxic and chronic toxicity may interfere and probably impair the use of the Salmonella/microsome assay to determine the potential of the area, showing the importance of assay association to evaluate potentially contaminated areas.