A modified model for a borehole ground heat exchanger borefield (BHE) of a ground-source heat pump (GSHP) system was developed based on a three-dimensional finite difference scheme which could cater for multiple ground layers and an inhomogeneous groundwater flow in the soil. The model was validated using FLUENT for a single borehole based on a constant load along the effective length of the borehole with good agreement. The present model was then used to investigate the effect of the groundwater table on the performance of the BHE. It was found that with the borehole partially-submerged in groundwater flow, the borehole specific load along the borehole depth became stratified, the extent of which depended on the various parameter values. The borehole thermal resistance also varied with the relative groundwater table and the groundwater flow velocity. The trends of the fluid temperature leaving a borehole were quite different between the situations when the borehole was partially-submerged in groundwater flow and the case with a full groundwater flow. This meant that the use of an effective groundwater flow velocity to account for the groundwater table effect in a full-groundwater-flow BHE model could be erroneous, particularly for simulation of a large BHE. (C) 2012 Elsevier Ltd. All rights reserved.