Abstract: Rural freshwater aquaculture is often constrained by a single energy supply structure, low renewable energy utilization, high sensitivity to environmental conditions, and high wastewater treatment cost. To address these problems, an optimal scheduling method for a rural integrated energy system considering water environment regulation was proposed. The objective of this study was to coordinate energy conversion, water-quality regulation, thermal comfort control, and aquaculture wastewater resource utilization within a unified day-ahead scheduling framework, thereby improving both economic performance and aquaculture safety. A freshwater shrimp aquaculture greenhouse was selected as the typical application scenario, and the coupling relationships among energy supply, pond-water temperature, dissolved oxygen, ammonia nitrogen, shrimp survival rate, and wastewater treatment were considered. First, a thermal balance model was established to describe the heat transfer process among indoor air, pond water, and the outdoor environment. Wall heat loss, glass heat loss, ventilation heat exchange, heat-pump regulation, and pond-air heat exchange were considered to characterize the thermal regulation process of the aquaculture greenhouse. On this basis, the effects of indoor-air thermal comfort and pond-water thermal comfort on system scheduling were analyzed. Second, a dynamic water-quality regulation model was developed. The ammonia-nitrogen concentration was modeled by considering shrimp excretion, residual feed decomposition, nitrification, and water exchange, while the dissolved oxygen concentration was modeled by considering shrimp respiration, oxygen supply, nitrification oxygen consumption, and water exchange. A shrimp survival-rate model coupled with dissolved oxygen and ammonia nitrogen was then constructed to quantify the influence of water-quality regulation on aquaculture safety. Third, a wastewater resource-utilization model integrating solid-liquid separation, temperature-controlled anaerobic digestion, gas storage, and energy conversion was established. The thermal demand of the biogas digester was also included to reflect the energy cost of maintaining anaerobic fermentation. Photovoltaic generation, power-to-gas equipment, an air separation unit, gas-fired equipment, and electric heating equipment were incorporated into the rural integrated energy system. Finally, a multi-objective optimal scheduling model was formulated to minimize operating cost and thermal comfort deviation while maximizing shrimp survival rate. A hybrid chaotic evolution optimization (CEO)-CPLEX solution framework was adopted, in which CEO handled nonlinear aquaculture-related decision variables and CPLEX solved the linear energy dispatch subproblem. Case studies showed that the proposed scheduling model effectively coordinated energy supply and water environment regulation in the aquaculture system. When indoor-air thermal comfort was further considered on the basis of pond-water thermal comfort, the total system cost increased by only 1.56%, indicating that improving the working environment of aquaculture personnel did not significantly increase the operating cost. Pond-water temperature remained within a narrow fluctuation range during the day-ahead scheduling period, which helped maintain the stability of the aquaculture environment. The coordinated regulation of dissolved oxygen and ammonia nitrogen maintained the shrimp survival rate above 90%, and the survival-rate penalty was effectively reduced under appropriate water-exchange and oxygen-supply strategies. The comparison of different nitrifying bacterial densities showed that increasing the density from 1×10⁷ to 5×10⁷ cells/m³ increased ammonia-nitrogen degradation from 2.51 to 3.54 g/m³, whereas a further increase to 1×10⁸ cells/m³ did not further improve degradation, indicating that 5×10⁷ cells/m³ was a suitable bacterial density under the case conditions. The water-exchange analysis showed that increasing the water-exchange ratio from 10% to 20% raised the total system cost from 9519 to 13346 yuan, while the survival-rate penalty decreased only from 231.4 to 159.4 yuan. This indicates that excessive water exchange increased heating, oxygen-supply, and water-purchase costs, but brought only limited improvement in the survival-rate penalty. Therefore, a 10% water-exchange ratio achieved a better balance between economy and aquaculture safety in the studied case. In addition, compared with the conventional wastewater treatment strategy, biogas fermentation reduced the total system cost by 22.2%, demonstrating the economic value of converting aquaculture wastewater into usable energy. The results also showed that the proposed framework could adapt to photovoltaic output fluctuations by adjusting external energy purchase and multi-energy conversion equipment while maintaining pond-water temperature within the specified limits and meeting oxygen-supply requirements. This study provides a coordinated scheduling framework for rural integrated energy systems in freshwater aquaculture scenarios. The proposed method can improve renewable energy utilization, reduce wastewater treatment cost, maintain water-environment stability, and support the management of shrimp survival rate. It also provides a theoretical basis and technical reference for the low-carbon, resource-oriented, and safe operation of rural aquaculture energy systems.