Heavy metals have an enduring presence, risky characteristics, and the propensity to accumulate in the environment. This is why heavy metal toxics are widely acknowledged as harmful environmental pollutants. Heavy metals damage both aquatic and terrestrial ecosystems, posing a major risk to the environment and human health. Four freshwater fish species namely Labeo rohita, Catla catla, Hypophthalmichthys molitrix, and Ctenopharyngodon idella were the focus of this investigation. This study investigated the potential genotoxic effects of lead (Pb), copper (Cu), and cadmium (Cd) on the above fish species through the application of comet assay test. The fish were exposed to these metals at four distinct concentrations (19%, 24%, 31%, and 50% of the LC50) over the course of 40 days. All four fish species were exposed to metals to varying degrees, according to the genetic damage index, cumulative tail length of comets, and the proportion of damaged cells. In contrast to Catla catla, Hypophthalmichthys molitrix had the highest prevalence of DNA damage. The current study suggests that the presence of these particular metals in Pakistan's aquatic ecosystems may have an adverse effect on the DNA of the country's fish species. Metals cause damage to DNA in fibroblast cells through distinct mechanisms when present in water, air, and soil. Comet assay test has a remarkable sensitivity that helps to identify extremely low amounts of DNA damage. Out of the four fish species, Ctenopharyngodon idella showed higher levels of damaged cells, a higher genetic damage index, and a cumulative comet tail length as compared to others. All four fish species experienced a significant increase in DNA damage, genetic damage index, and comet tail length at 50% concentration of metals LC50.