A large number of methods have been applied to evaluate genotoxic damage in different aquatic species. Comet assay, as a method for detecting DNA alterations, and micronucleus test, as an index of chromosomal damage are the most widely used and authentic methods in laboratory and field studies. The primary objective of the study was to evaluate the genotoxic effects of heavy metals generated by toxic industrial effluents and various kinds of pollutants from urban and agricultural areas and domestic waste on Catla catla and Cirrhinus mrigala due to water pollution in the Chenab River, Pakistan. The heavy metals Cd, Cu, Mn. Zn, Pb, Cr, Sn, and Hg were detected by atomic absorption spectrophotometry from water samples collected from predetermined sampling sites. All the physicochemical parameters and heavy metals were found to exceed the upper limits recommended by various agencies. Comet assays showed significant (p < 0.05) DNA damage in C. mrigala compared to C. catla for tail length and olive tail moment from three different sites. Significant (p0.05) findings were observed between fish collected from farmed and non-polluted upstream waters. Micronucleus assays showed similar findings for single and double micronucleus induction in C. catla and C. mrigala. A significantly (p < 0.05) higher micronuclei induction and percent tail DNA was observed in C. mrigala specimen collected from the polluted site. These findings infer that DNA damage could be used as a biomarker of pollution load and its early monitoring by using simple and reliable techniques such as the comet and micronucleus assays, expedient methods for toxicity screening of aquatic environments. Regular monitoring is necessary to assess eco-health of the Chenab River by choosing perhaps C. mrigala, being a bottom feeder, as a bioindicator that could provide more reliable information to determine the status of the environmental quality of the river.