Recently, however, concern about aquatic environmental pollution has increased, especially in respect to aquatic water bodies such as rivers. Municipal wastewater comprises 99.9% water with small concentrations of dissolved and suspended organic and inorganic solids. Among organic substances, there are synthetic detergents, soaps, fats, proteins, carbohydrates, lignin and their decomposition products. Natural and synthetic (organic and inorganic) chemicals also add major toxic compounds from industry. These types of water pollution directly and indirectly influence aquatic life by modifying genomes. The objective of this study was to evaluate the effect of anthropogenic pollution on DNA damage and the fatty acid profile of the bottom dweller fish (Cirrhinus mrigala), collected from the River Chenab, in order to assess the effect of the toxicants on the quality of the fish meat. The levels of Cd, Hg, Cu, Mn, Zn, Pb, Cr and Sn and of phenols from this river were significantly higher than the permissible limits set by the USEPA. Comet assays showed DNA damage in Cirrhinus mrigala collected from three different sampling sites in the polluted area of the river. Significant differences were observed for DNA damage through comet assay in fish collected from polluted compared to control sites. Non-significant differences were observed for DNA damage between farmed and fish collected from upstream. The micronucleus assay showed similar trends. Fish from the highly polluted site showed fewer fatty acids and more saturated fatty acids in their meat compared to fish from less-polluted areas.