Heavy metals have animmense impact on aquatic ecosystems, and their toxic effects are transferred to the inhabiting organisms. Experiments were conducted to investigate the health of snow trout Schizothorax esocinus inhabiting Dal Lake. Heavy metals (Cd > Ni > Cu > Cr) were found to accumulate in the major immune organs of the fish (head kidney, liver, spleen, thymus) which led to change in the overall physiology. The head kidney, liver, and spleen of a fish contain high amount of these metals. The least accumulation of these metals was found in the blood, whereas Cd and Ni were completely absent in the integument. Hepatic marker enzymes (aspartate aminotransferase (AST), alanine aminotransferase (ALT), and alkaline phosphatase (ALP)) were normal, while the renal marker enzyme creatine kinase showed marked difference in its value. The cortisol level was normal, while immunoglobulin M showed elevated level representing active immunity. At a cellular level, the histopathology of immune organs showed marked damage. Metallothionein (MT) and glutathione peroxidase (GPX) genes showed variable expression pattern in the immune organs with the head kidney showing the highest expression of both the genes, and blood showed the least. We observed that the aquatic plants (Nelumbo nucifera and Trapa natans) inhabiting the lake played an important role in phytoremediation. An integrated approach involving biochemical, hematological, genotoxic, and histopathological studies can provide a valuable information to understand fish adaptive patterns and monitor water quality.