Water quality in land-based fish production can be controlled through either instantaneous water exchange or costly wastewater treatment followed by recirculation. Agricultural-aquaculture integration is an excellent alternative technique for lowering nutrient discharge levels, increasing profitability, and transforming fish culture wastewater into valuable products. The current study employed a solar energy system to power two separate IMTA-aquaponics systems (Nutrient Film Technique, NFT, and Floating Raft Systems, FRS) for the cultivation of Nile tilapia, African catfish, thin-lipped grey mullet, freshwater crayfish, freshwater mussels, and a variety of vegetables. Tilapia and catfish were fed exclusively on diets under the IMTA system. All wastewater from tilapia and catfish ponds, including dissolved and solid, flows sequentially to ponds of other cultivated species. The water then flows through the IMTA system's terminal point to the NFT and FRS systems before returning to the tilapia and catfish ponds, with complete control of the nutrient flow throughout this entire circular system. Two 147-day production cycles were carried out. The findings of the second production cycle are presented. Total biomass gain for aquatic species in the IMTA system was 736.46 kg, compared to 145.49 and 271.01 kg in the tilapia and catfish monoculture systems, respectively. The current IMTA system had a cumulative feed conversion ratio (FCR) of 0.90, whereas monoculture systems for tilapia and catfish had FCRs of 1.28 and 1.42, respectively. Nile tilapia and catfish consumed 571.90 kg of feed containing 25.70 kg of nitrogen (N) and 9.70 kg of phosphorus (P), respectively, and gained 11.41 and 3.93 kg of dietary N and P, representing 44.40 and 40.46% dietary N and P retention, respectively. In the IMTA system, the addition of mullet and prawn as detrivores aquatic animals improves dietary N and P utilization efficiency to 59.06 and 51.19%, respectively, and the addition of mussels as herbivore animals improves dietary N and P utilization efficiency to 65.61 and 54.67%, respectively. Finally, the use of FRS and NFT as hydroponic systems increased dietary N and P efficiency to 83.51% N and 96.82% P, respectively. This study indicates that the IMTA-Aquaponic system, as a bio-integrated food production system, can convert the majority of fish-fed residuals into useful products suitable for desert, rural, and urban areas in poor and developing countries.