The role of water in our daily lives cannot be highlighted enough, and ensuring the availability of pure water is an urgent need. Bleaching powder (calcium hypochlorite) and Strychnos potatorum Linn. seeds are commonly used in water purification as a disinfectant and anticoagulant, respectively, yet their safety levels have not been analyzed so far. Hence, a genotoxic assessment was conducted using Allium cepa chromosome aberration assay. Reduction in mitotic index and increase in abnormality percentage was observed for both, but this effect was dose dependent. All values were statistically significant at p<0.05%. Bleaching powder was found to be cytotoxic and genotoxic compared with the control. Abnormality percentage was found to be significantly high when compared with the positive control. Chromosome aberrations like binucleate condition, micronuclei formation, stickiness, and lesions could only be observed in root meristems treated with positive control and bleaching powder. The seeds of S. potatorum expressed mild cytotoxicity, but the genotoxic effect was found to be negligible when compared with positive control. Other chromosome aberrations observed included chromosome bridges, c-metaphases, chromosome laggards, shift in microtubule organizing centre, polyploidy, early movement of chromosomes, vagrant chromosomes, as well as diagonal, disturbed, and scattered arrangement of chromosomes. Thus, the genotoxic effect of bleaching powder warns people to use a safer choice of S. potatorum in water purification, whenever possible, as in the condition of muddy, coagulated water.