Numerical solutions of the coupled equations of fluid flow and heat transport are used to investigate how the near-surface thermal regime is perturbed by groundwater flow in a basin with a three-dimensional water table configuration. We consider specifically those conditions where the hydraulic gradient on the water table drives the flow system, thermally induced buoyancy forces modify but do not control the flow field. The hydrologic disturbance of the thermal field and the significance of a water table gradient transverse to the regional slope depend upon the interplay of the three-dimensional water table configuration, the basin geometry including the depth to the basal impermeable boundary, the anisotropy, and the permeability of the subsurface formations. These factors act together to determine groundwater flow patterns, depths of circulation along individual flow lines, and areal distribution of groundwater recharge and discharge. The uniformity of surface heat flow values determined from a series of shallow boreholes in an advectively disturbed regime will depend on the location of the measurement sites relative to the hinge line separating areas of groundwater recharge and discharge and on the extent of the region centered about the hinge line where fluid inflow/outflow rates are insufficient to perturb the thermal field.