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Effect‐based analyses are being recognized as excellent tools to a comprehensive and reliable water quality evaluation to complement physical and chemical parameters. The Salmonella /microsome mutagenicity test was introduced in the São Paulo State water quality‐monitoring program in 1999 and waters from 104 sites used to the production of drinking water were analyzed. Samples were tested after organic extraction, using the microsuspension version of the Salmonella /microsome assay with strains TA98 and TA100 with and without S9‐mammalian metabolic system. Of the 1720 water samples analyzed in 20 years, 20% were positive; TA98 was the most sensitive strain, detecting alone 99%. Results were presented in hazard categories to facilitate water managers' understanding and general public communication. Hot spots of mutagenicity were identified, and pollution sources investigated. A flow scheme with instructions of how to proceed in case of mutagenic samples was developed and implemented in the monitoring program. Enforcement actions were taken to reduce exposure of humans and aquatic biota to mutagenic compounds. The results presented provide scientific basis for the incorporation of the Salmonella /microsome assay in a regulatory framework, and to guide water‐quality managers. The inclusion of a mutagenicity assay using standardized conditions proved to be an opportunity to improve the quality of water, and the strategy presented here could be applied by any environmental agency around the world. Environ. Mol. Mutagen. 61:200–211, 2020. © 2019 Wiley Periodicals, Inc.
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