This study was conducted to assess the effect of heavy metals (Cd, Hg, Cu, Mn, Zn, Pb, Cr, and Sn) on the fatty acid profiles of Catla catla, Labeo rohita, and Cirrhinus mrigala collected from two polluted sites in the Chenab River and Jhelum River (non-polluted site). The heavy-metal levels were determined using atomic absorption spectrophotometry. The results showed that the levels of Cd, Hg, Cu, Mn, Zn, Pb, Cr, and Sn in the river water exceeded the permissible limits recommended by various international agencies. Some important fatty acids were not detected in the muscle samples of the fish species collected from the highly polluted site (HPS). Caprylic acid (C8:0) and lauric acid (C12:0) were undetectable in Catla catla and Cirrhinus mrigala. Palmitoleic acid and eicosapentaenoic acid were present in Catla catla alone, and they were not found in Labeo rohita and Cirrhinus mrigala harvested from a less polluted site (LPS). More saturated fatty acids and less fatty acids were detected in the muscle samples of Catla catla, Labeo rohita, and Cirrhinus mrigala collected from HPS than in those collected from LPS. The untreated discharge of domestic and industrial waste probably causes a reduction in the fatty acids in the biomass of microalgae and zoobenthos and, ultimately, adversely affects the upper links of the food chain in the river. (C) 2018 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.