Continuously feed-based aquaculture leads to excessive nitrogen and phosphate loads, degrading the culture environment. In this study, lotus (Nelumbo nucifera Gaertn) was planted in yellow catfish (Pelteobagrus fulvidraco Richardson) culture ponds to construct an integrated agriculture–aquaculture system to reduce nutrient accumulation and remediate the aquacultural environment. Results showed that additional lotus cultivation significantly reduced TN and TP concentrations in the pond water by 51.81% and 34.68%, respectively. Meanwhile, the concentrations of NH4+-N, TN, and TP in the sediment of co-culture ponds significantly decreased by 54.12%, 8.55%, and 10.85%, respectively, at the conclusion of the experiment period. Additionally, with the growth of lotus, the co-culture ponds exhibited significantly lower nitrogen and phosphorus fluxes across the sediment–water interface. Spearman correlation analysis revealed a significant positive correlation between the NH4+-N flux and TN concentration in the water and between TN flux and NO3−-N concentration in the water, respectively. This study suggests that the lotus-fish co-culture offers an optimal integrated agriculture–aquaculture system capable of mitigating excessive nutrient loads and improving the aquacultural environment.