Kyo-machiya is a type of traditional residence in Kyoto, Japan. These houses are the principal component of the streetscape in Kyoto City. In accord with the Japanese national carbon neutralization goal and the city ordinance on Kyo-machiya preservation and regeneration, an energy-saving renovation plan for achieving a net-zero energy community for Kyo-machiya is under discussion. Most Kyo-machiya have a shallow well, where utilizing the well water as the heat source for a groundwater heat pump (GWHP) is feasible. However, the efficiency of the heat pump decreases with continual operation due to the decrease of the water temperature. In previous research, a drainage pump was used to increase the heat-replenishment speed, which increased the efficiency of the heat pump. However, due to the small water storage capacity of the well, the drainage pump had to work intermittently, which limited the improvement. In this study, we similarly tried to improve the efficiency of the heat pump by drainage, but instead of conducting this process in the heat exchange well, we utilized the drainage in one or more downstream well. With this strategy, the possible drainage duration was unlimited because the process can be executed in a few wells alternately or simultaneously. The strategy is simulated herein using a finite difference model. The results showed that the strategy is effective within a certain distance. With this improved strategy, the GWHP-drainage system in the community is expected to work coordinately, and energy costs for air-conditioning in the community are expected to be decreased.