In this paper we discuss temperature anomalies that develop in the shallow subsurface as a result of localized deforestation in combination with shallow horizontal groundwater flow. Model results show how a patch-wise pattern of deforestation at the surface induces significant lateral temperature gradients in the subsurface. Results also indicate that lateral heat transport by advection via horizontal groundwater flow becomes significant above flow rates of about 10−8 m/s. In a steady state situation, reached 1750 a after deforestation, an anomaly of 0.1 K is still present at a distance of ∼2.5 km downstream of the deforested patch at depths between 200 and 575 m for horizontal groundwater flow velocities between 10−7 m/s and 10−8 m/s, respectively. We carried out transient simulations to examine the impact of deforestation on subsurface temperatures during the last century. These experiments include a study of the effects of regional surface warming on the thermal regime of the subsurface. In these scenarios, 100 a after localized deforestation, significant temperature anomalies occur hundreds of meters downstream of the deforested areas. Results show that ground surface temperature history reconstructions based upon synthetic temperature versus depth profiles up- and downstream of the deforested patches fail to recover the timing and magnitude of the warming event imposed at the surface. Results from our numerical simulations indicate that lateral heat flow effects should be considered when using subsurface thermal data for constraining land surface schemes in general circulation models.