Heat flow shifts between 20 and 60 mW/m2 in the upper ∼2 km of the crust and 60 to 150 mW/m2 at greater depth have been observed in the Soumagne, Havelange and Grand-Halleux deep wells, all located close to the Variscan thrust front in Belgium. We have gathered geologic, hydrogeologic, thermal and paleoclimatic data and have used them to perform large-scale 2-D coupled hydro-geothermal modelling of the current temperature and heat flow distribution in the area. Calibration of the models was performed with temperature data from the three wells, and requires considerable variations in basal heat flow or heat production. Model results from several scenarios including different processes confirm that cooling by groundwater is the dominant control on the heat flow shift observed in the upper ∼2 km depth in the three boreholes; the groundwater influence, both pervasive and along major conduits, is rivalled by paleoclimatic influence only in the Grand-Halleux well. The major cooling effect by groundwater requires less than 0.5 Myr and is controlled by the present geomorphology.