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Teleosts are the largest class of bony fishes and account for more than 90% of fish species. Their reproductive systems are the key feature to adopt gradual evolutionary change under aquatic environmental conditions. Aquatic ecosystems are faced with a serious threat to their proliferation due to the discharge of untreated industrial effluents into them. Here, scanning electron microscopy (SEM) was used to examine the damaged ovaries of the freshwater fish Rohu, Labeo rohita (Hamilton-Buchanan), due to their exposure to different heavy metals in the polluted waters of Harike Wetland in Punjab, India. Deformed oocytes with rough and distorted surfaces were observed in SEM. Microscopic analysis showed that environmental pollution caused by municipal effluents had damaged the microstructural surface on the fish ovaries. Energy-dispersive X-ray spectroscopy also showed damage of the microstructural surface and an abnormal deposition of heavy metals. The alterations in the reproductive system of the fish appeared to be the most responsive and a reliable indicator of environmental pollution, which indicates their significance in aquatic biomonitoring systems. This is the first report in North India showing tissue level markers in biomonitoring programs using the ovary of Labeo rohita as the model system. Microscopic analysis showed that environmental pollution caused by municipal effluents damaged the microstructural surface of the fish ovaries. [ABSTRACT FROM AUTHOR]