The aim of this research was to study at a pilot plant the influence of peracetic acid (PAA) on the formation of mutagenic compounds in river waters used for human consumption. The results obtained using PAA were compared to those for the most commonly used disinfectant, sodium hypochlorite (NaClO). Ames test and three genotoxicity plant tests, Allium tests and Tradescantia/micronuclei (TRAD/MCN) test, were used to evaluate the mutagenic activity of disinfected water samples. Chemical analysis, using gas chromatography/mass spectrometry (GC/MS), was also performed to identify disinfection by-products (DBPs). A slight bacterial mutagenicity was found in raw river water and similar activity was detected in disinfected water samples. Plant tests gave genotoxicity only for raw river water. DBPs identified in PAA-treated water included carboxylic acids, a few non-halogenated alcohols and carbonyl-containing compounds, whereas some potentially mutagenic halogenated by-products were found in NaClO-treated samples. Although PAA appears to be promising for water potabilization, these results must be confirmed with different source waters and with higher concentrations of PAA.