Aquaponics combines the advantages of aquaculture and hydroponics as it suits the urban environment where a lack of agricultural land and water resources is observed. It is an ecologically sound system that completely reuses its system waste as plant fertilizer. It offers sustainable water savings, making it a supreme technology for food production. The two major processes that hold the system together are nitrification and denitrification. The remains of fish in form of ammonia reach the bio filters where it is converted into nitrite and further into nitrate in presence of nitrifying and denitrifying bacteria. Nitrate eventually is taken up by the plants. However, even after the uptake from the flow stream, the effluent contains remaining ammonium and nitrates, which cannot be directly released into the environment. In this review it is suggested how integrating the biofilm-based bioreactors in addition to aquaculture and hydroponics eliminates the possibility of remains of total ammonia nitrogen [TAN] contents, leading to bioremediation of effluent water from the system. Effluent water after releasing from a bioreactor can be reused in an aquaculture system, conditions provided in these bioreactors promote the growth of required bacteria and encourages the mutual development of plants and fishes and eventually leading to bioremediation of wastewater from aquaponics.