In the Netherlands the present-day thermal gradient in the shallow subsurface (i.e. the upper few 100 m), is around 20°C km–1, whereas at depths between 0.5 and 3 km it is ∼33°C km–1. This large contrast in the gradient between shallow and deeper parts of the subsurface occurs throughout the country and cannot be explained by either systematic thermal property changes with depth or the depositional setting of the region. In this paper we use a 1D thermal model for the crust and demonstrate that this observed temperature-depth trend most likely reflects a transient condition inherited from past climate change. It is shown that the prolonged cold period during the Weichselian (∼110–10 kya) and the subsequent warmer conditions during the Holocene account for the increase in the thermal gradient with depth. Moreover, we demonstrate that thermal history further back in time still influences the present-day subsurface temperature. Geothermal climate-change influences on these long time scales have not been documented before for the Netherlands.