The present article highlights a dual sustainable approach towards the rejuvenation of water bodies and food waste management by utilizing bio-enzymes and its byproducts. Environmental pollution is rising drastically due to excessive use of harmful chemicals causing degradation of our ecosystem. Most of these chemicals are often found in water bodies even after sewage treatment and possess harmful threats on the environment as well as on the human body. The use of bio-enzymes, organic solutions made from citrus fruit peels through a natural process, can be considered as an eco-friendly as well as cost effective solution to these hazardous chemicals. We attempt here to demonstrate how to restore and rejuvenate water bodies using bio-enzymes prepared from Citrus Fruit peels and tried to explore how it affects water quality parameter indices, such as, hardness, alkalinity, chloride ion concentration etc. Water quality parameters are measured for water samples with and without the bio-enzyme at different time intervals. Our study shows a marked improvement in the water quality parameters that not only reveals the potential use of the bio-enzyme on water treatments but also enables the whole treatment to be cost effective and eco-friendly. Moreover, the organic residue derived during the preparation of bio-enzymes can be further used as good quality manure which can improve the soil quality instead of using harmful chemical fertilizer and thus demonstrates an efficient and effective way towards the management of food wastes across the ecosystem