The genotoxicity of industrial wastewater samples from Aligarh and Ghaziabad cities was compared using the Ames plate incorporation test, the Ames fluctuation test and the Allium cepa test. While TA102 and TA104 strains exhibited the highest sensitivity against the Aligarh sample (AWW) in terms of the slope (m) of the dose–response curve in the plate incorporation assay, TA98 and TA97a were the most sensitive strains based on the induction factor, Mi(p). TA98 once again, was the most sensitive strain against the test sample from Ghaziabad (GWW) in terms of ‘Mi(p)’ while TA102 was the most sensitive strain on the basis of the slope (m). TA100 displayed the highest susceptibility towards the samples from Aligarh in the fluctuation test. However, TA102 and TA98 responded maximally to GWW in this bioassay. The mutagenicity of the test samples seemed to be partly mediated by reactive oxygen species (ROS) as evidenced by the use of free radical scavengers. Mannitol brought about the maximum decline in the number of revertants of TA102 by the Aligarh sample, whereas such a reduction in case of Ghaziabad sample was exhibited with superoxide dismutase. Both the test water samples induced various anaphase aberrations in the root cells of Allium cepa. Fragmentation of the chromosome was the predominant effect of the Aligarh water sample while the Ghaziabad sample induced chromosome stickiness. The crucial roles of heavy metals and pesticides in the genotoxicity of AWW and GWW, respectively, have been suggested. In view of the problem associated with the interpretations of data, we recommend that all the test bioassays should be carried out in the presence of ROS scavengers for the fool proof evaluation of the genotoxicity of water samples.