The study presents the first application of the Connected Linear Network (CLN) package implemented in MODFLOW-USG to an existing Ground-Source Heat Pump (GSHP) system. The numerical element was specifically adapted by the authors in a previous study to simulate vertical Borehole Heat Exchangers (BHEs) and is here applied for the first time to evaluate the heat transfer in Milano subsurface induced by a GSHP system. The evaluation of interference between geothermal systems and wells is an important topic, especially in densely populated areas, which has scarcely been explored in the literature. Specifically, the aim is to evaluate the thermal perturbation and the possible interference between BHE systems and the drinkable water wells of the Armi pumping station managed by MM S.p.A. The simulation results show moderate groundwater thermal perturbation: approximately 3 °C at 100 m downgradient of the borefield and, furthermore, a limited impact (maximum 1 °C) in just two wells of the Armi pumping station. After 3 years of GSHP system operation, the thermal perturbation can extend for kilometers, but with limited variation in groundwater temperature (lower than 1 °C). Although the predicted groundwater temperature variation is not critical, the real-time monitoring of temperatures coupled with numerical modeling is essential to prevent thermal interference and optimize GSHP system performance.