Lakes are vital to the upkeep of the environment because they regulate river water flow and act as a source of water during dry seasons. Aquatic environments affected by sewage effluents usually show the release of a complex mixture of xenobiotics, which can impact important fish physiological aspects. Monitoring aquatic ecosystems, especially significant lakes, is crucial for ensuring the availability of aquatic resources. Kerala lakes are under anthropogenic stress, mostly as a result of the ongoing sewage influx and agricultural runoff that change the chemical composition of the water. To detect the presence of the pollutants, biomonitoring techniques employ a range of cellular, biochemical, and histopathological indicators. To ascertain the harmful consequences of contaminants, these biomarkers are included in monitoring programs. The current paper provides a summary of the evolution and use of fish histopathology as biomarkers. Because fish are primarily influenced by the water quality. The goal of the current study was to assess the variations in the histopathological alterations in the muscles and gills of fish in Kerala's Lake Chakkamkandam.Degeneration in muscle bundles with specific areas of necrosis, atrophy and edema of muscle bundles, were all observed histologically in the muscles of both fish. Proliferative, degenerative, and necrotic changes in the epithelium of gill filaments and edema in secondary lamellae, dilatation and congestion in gill filament and mucous cell proliferation were among the pathogenic abnormalities in the gills. The environmental contamination of Lake Chakkamkandam, it was determined, caused a number of histological changes in the tissues of Oreochromis mosambicus and Mugil cephalus. The results suggest that the selected biomarkers can be used to assess the consequences of pollution in naturally occurring aquatic ecosystems. The anthropogenic activities related to agriculture, human habitation, and tourism activities in the city have an impact on water quality. The morphological results of the current study emphasise the value of histopathology analysis in biomonitoring programmes for evaluating water quality and the environment.