Heat advection by groundwater flow is known to improve the performance of ground heat exchangers (GHEs), but the effect of groundwater advection on performance is not yet fully understood. This numerical study examined how parameters related to groundwater flow, such as aquifer thickness, porosity, lithology, and groundwater flow velocity, affected the performance of a borehole GHE. Under a thin-aquifer condition (10 m, or 10% of the entire GHE length in this study), groundwater flow velocity had the greatest effect on heat flux. At a groundwater flow velocity of at least 10−4 m/s through a low-porosity aquifer filled with granite gravel with high thermal conductivity, the heat flux of a GHE was as much as 60% higher than that of a GHE in a setting without an aquifer. If the aquifer was as thick as 50 m, the high thermal conductivity of granite gravel doubled the heat flux of the GHE at a groundwater flow velocity of at least 10−5 m/s. Thus, not only groundwater flow velocity but also aquifer thickness and thermal conductivity were important factors. However, groundwater seldom flows at such high velocities, and porosity, gravel size and composition, and aquifer thickness vary regionally. Thus, in the design of ground source heat pump systems, it is not appropriate to assume a large groundwater effect.