The performance of ground-coupled heat pump systems (GCHPs) operating under significant groundwater flow can be difficult to predict due to advective heat transfer in the subsurface. This is the case of the Carignan-Salières elementary school located on the south shore of the St. Lawrence River near Montréal, Canada. The building is heated and cooled with a GCHP system including 31 boreholes subject to varying groundwater flow conditions due to the proximity of an active quarry being irregularly dewatered. A study with the objective of predicting the borehole temperatures in order to anticipate potential operational problems was conducted, which provided an opportunity to evaluate the impact of groundwater flow. For this purpose, a numerical model was calibrated using a full-scale heat injection test and then run under different scenarios for a period of twenty years. The heat exchange capacity of the GCHP system is clearly enhanced by advection when the Darcy flux changes from 6 × 10−8 m s−1 (no dewatering) to 8 × 10−7 m s−1 (high dewatering). This study further suggests that even the lowest groundwater flow condition can be beneficial to avoid a progressive cooling of the subsurface due to the unbalanced building loads, which can have important impacts for design of new systems.