In order to improve the water delivery capacity of the middle route of the South-to-North Water Diversion Project in winter, the technology of pumping well water to melt ice was previously adopted to improve the water temperature of the channel. In order to protect the local ecology and channel water quality during the process of pumping and recharging, this paper has analyzed the optimal limit to the range of groundwater level fluctuations and groundwater temperature fluctuations. The Baiquan Underground Reservoir was considered as the research object, and a three-dimensional numerical model of hydrothermal coupling was established. Correlation analyses of pumping and recharge capacity with various factors, and between temperature changes after recharging and various factors, were carried out with a view to protecting local water quality. The single well pumping and recharging scheme was optimized by genetic algorithm. The quantitative estimation formula of pumping and recharge water capacity, and the well depth, permeability coefficient, initial water level, and duration of continuous pumping and recharge, as well as the recovery water level variation formula, were established under the limitation of water level fluctuation. The quantitative relationship between horizontal maximum diameter, L, and the recharge flow rate, the continuous recharge duration, vertical maximum depth, H; and the well depth, temperature change rate, K, and the recharge water temperature, were obtained. The results showed that the permeability coefficient and soil thermal conductivity had little effect on the temperature field change. Additionally, recharge should be carried out in summer, when the temperature of recharge water is above 14.8 °C. When the number of pumping or recharging times, n, is two, the total amount of pumping or recharging during the operation period reaches its maximum. Compared with continuous operation during the operating period, this report found that the total amount of pumped water would increase by 1.1 × 106 m3, and the total amount of recharge would increase by 7 × 105 m3.