The pollution of the river by man-made sewage and waste disposal is not only harmful to animals and plants in it but also for animals higher in the food chain including those close to the food chain. Water is the most vital natural substance, as it plays a role in nearly every aspect of human life. Therefore, there is a great need to ensure that the water used by humans should not contain hazardous substances. Water quality is directly linked to biological life. The Nag River flows from the Lava village of north Ambazari Lake and flows into the center of Nagpur city. As a result of rapid and unstoppable development, significant changes have taken place in the water quality of the Nag River. Because the Nag River’s water is frequently used for irrigation, it should be tested for cytotoxicity and genotoxicity. Since the rate of cancer and genetic disorders has recently increased in the Nagpur region, the Nag River’s water could be a source of carcinogens in the food chain, affecting the population. This study was conducted to analyze the impact of water collected from various points of the Nag River using Allium cepa as a model organism. The results of this study showed that all water samples from the Nag River cause a cytotoxic effect (20-23%) and genotoxic effects (23-28%) in Allium cepa cells. Therefore, before the use of Nag River water, it must be treated to diminish its harmful effect.