New temperature measurements from eight boreholes in the West African Craton (WAC) reveal superficial perturbations down to 100 m below the alteration zone. These perturbations are both related to a recent increase in the surface air temperature (SAT) and to the site effects caused by fluid circulations and/or the lower conduction in the alterites. The ground surface temperature (GST), inverted from the boreholes temperatures, increased slowly in the past (~0.4 °C from 1700 to 1940) and then, more importantly, in recent years (~1.5 °C from 1940 to 2010). This recent trend is consistent with the increase of the SAT recorded at two nearby meteorological stations (Tambacounda and Kedougou), and more generally in the Sahel with a coeval rainfall decrease. Site effects are superimposed to the climatic effect and interpreted by advective (circulation of fluids) or conductive (lower conductivity of laterite and of high-porosity sand) perturbations. We used a 1-D finite differences thermal model and a Monte-Carlo procedure to find the best estimates of these site perturbations: all the eight borehole temperature logs can be interpreted with the same basal heat-flow and the same surface temperature history, but with some realistic changes of thermal conductivity and/or fluid velocity. The GST trend observed in Senegal can be confirmed by two previous borehole measurements made in 1983 in other locations of West Africa, the first one in an arid zone of northern Mali and the second one in a sub-humid zone in southern Mali. Finally, the background heat-flow is low (31±2 mW m−2), which makes this part of the WAC more similar with the observations in the southern part (33±8 mW m−2) rather than with those in the northern part and in the Pan-African domains where the surface heat-flow is 15–20 mW m−2 higher.