Inefficient monitoring of the water resource recovery facility at various health care establishments may lead to detrimental effects on human population, especially when such water get mixed with potable municipal water supply. To ensure the efficiency and proper functioning of the water resource recovery facility and quality of water, before it being disposed of, the present study was conducted with the assessment of physico‐chemical parameters of water and its genotoxic and cytogenetic effects in mice. The sample water was given ad libitum to animals for three different time durations, that is, 7, 15, and 30 days. Bone marrow chromosomal aberration and bone marrow micronucleus (MN) assay were performed to get the extent of genotoxicity and cytogenicity. The results showed presence of chromosomal aberrations like fragments breaks and ring formation in different groups. Besides this, a significant (p < 0.05*, p < 0.01**, p < 0.001***) decrease in the mitotic index was noted in the group which was given 100% concentrated sample water for 30 days. A significant (p < 0.05*, p < 0.01**, p < 0.001***) increase in MN induction and decreased ratio of polychromatic to normochromatic erythrocytes were observed in groups which were given samples at 10% and 100% concentrations for longer durations. The findings suggest that even the recovered sample water reflects a positive in vivo genotoxic potential when given for a longer duration of 30 days, indicating some lacuna in the treatment process.