Altitudinous levels of toxic chemicals from Faisalabad city are disposed of directly into Chenab River through Chak Bandi Main Drain (CMD). The present study aimed to determine the degree of changes in the histological architecture of the liver, gills, kidneys, and muscles of fish Oreochromis niloticus collected from different polluted river sites. Fish samples collected from the Faisalabad fish hatchery and upstream to CMD acted as a control. Metabolically vital organs were subjected to histopathology. Necrosis, hemorrhage, and epithelial hyperplasia were observed in the gills of fish inhabiting the River downstream to the CMD entrance. Liver tissues were found to be affected by vacuolated cytoplasm, bile duct proliferation, melanomacrophages, and necrosis. In kidney tissues, Shrinkage of the renal cortex, necrosis, and destructive renal tubules was observed. Histopathology of muscles indicates the presence of hypertrophy and swollen myofibers. In contrast, upstream specimens of fish exhibited mild tissue alterations. Histopathology of gills tissue showed vacuolization. Liver tissues indicated the presence of hypertrophy and more frequent kupffer cells than usual. The vacuolation was observed in kidney tissues. Muscle tissues expressed splitting of muscle fibers and degeneration in muscle bundles. However, sections of tissues collected from farmed fish have normal morphology and no anomalies. The histopathological assessment indicated various cellular, biochemical and histological changes in response to the contamination in the vicinity of the fish. Such alternations can be used as a monitoring tool for freshwater contamination and the whole population’s health in the ecosystem.