The sustainable development of aquaculture faces a significant challenge due to the need for the frequent treatment of aquacultural waste. This research presents a pioneering solution by concurrently utilizing aquacultural waste to produce biochar and enhancing a sediment microbial fuel cell (SMFC)’s treatment efficacy for waste generated from the integrated multitrophic aquaculture (IMTA) system. The water quality parameters of the aquacultural pond water were analyzed, and synthetic wastewater was prepared to validate the system’s efficiency. Over a period of more than 50 days, the SMFC was operated and monitored, yielding an average chemical oxygen demand (COD) removal efficiency of 86.31 ± 2.18%. The maximum operating voltage of the SMFC reached 0.422 V on the 21st day of operation when connected to an external resistance of 975 Ω. A novel-activated aquacultural biochar catalyst was synthesized from aquaponics waste and used as a cathode catalyst, substantially improving the SMFC’s performance. Characterization studies demonstrated that the aquacultural biochar catalyst was an active electrocatalyst, accelerating the oxygen reduction reaction rate and leading to increased power output and overall efficiency of the SMFC. The SMFC utilizing the aquacultural-waste-based biochar cathode catalyst showcased the highest maximum power density, with a range of 101.63 mW/m2 (1693.83 mW/m3), and the lowest internal resistance, indicating superior performance. These results validate the reliability of implementing SMFCs in actual aquaculture systems. A novel modular design for SMFC reactor-assisted small-scale integrated poultry–fish culture systems is proposed for further practical application in real-life aquaculture settings. This research contributes to finding sustainable and effective methods for waste treatment for aquaculture, promoting the development of environmentally friendly practices in the industry.
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