Poondi Lake, the major reservoir that supplies water for the metropolitan city Chennai should be devoid of pollution. Even though, the water is treated in prior to the supply, it is mandatory to check the quality of freshwater ecosystem in a periodic manner. Hence, this study is conducted to assess the water quality of Poondi Lake. The results suggest that even though there is presence of Gram-negative rods and Gram-positive cocci in the water and sediment levels, the colony count were under permissible levels. This ensures that the quality of water is safe and potable for humans. The proximate analysis, relative organ weight index, biomarker analysis, enzyme and protein analysis in the bio-indicator species Oreochromis niloticus confirms that the freshwater ecosystem of Poondi Lake reservoir is of good quality and the impact of pollution is less. But further analysis at the molecular level will depict the actual scenario of pollution in long term effect. To conclude, periodic assessment of fresh water ecosystem should be done to evaluate and prevent the pollution of freshwater. Even though pollution has an impact on the macromolecules, evaluating at genetic levels gives us a clear picture on the effect of pollution on fresh water biota.