The intensification of koi fish farming increases the accumulation of organic waste, resulting in decreased water quality and high mortality. Therefore, a more efficient and adaptive ecotechnological approach is required. This study aimed to evaluate the performance of a dual-mode (aerobic–anaerobic) bioreactor based on indigenous microbes in koi fish farming. Three treatments were used in this study: control (without circulation), RAS (recirculation without a bioreactor), and a dual-mode bioreactor. The bioreactor was constructed with four layers of media (cotton fiber, bio-ball, PVA sponge, and zeolite) and operated using continuous flow. The water quality parameters measured included COD, TOM, nitrate, DO, pH, TDS, EC, total bacterial count (TPC), and fish survival rate. The results showed that the bioreactor provided the most significant reduction in COD from 16.63 to 4.30 mg L⁻¹ and reduced TOM to 14.00 mg L⁻¹, while the control and RAS experienced accumulation of organic matter. The consistent increase in nitrate in the bioreactor (up to 12.43 mg L⁻¹) was accompanied by a strong negative correlation with TOM (R² = 0.9971), indicating the dominance of ammonification and nitrification. DO and pH parameters remained stable in the bioreactor, whereas TDS increased more slowly than in the other two treatments. The TPC was higher in the aerobic column than in the anaerobic column. The improvement in water quality in the bioreactor directly affected koi survival, which reached 93.3%, higher than that in the RAS (75%) and control (25%). This study indicates that the dual-mode bioreactor has the potential to be an ecotechnological solution for waste management in small-to medium-scale koi farming. Further testing is recommended to evaluate the long-term performance and stability of microbial communities under varying waste loads