A quantitative budget estimate of actual evapo-transpiration is a key issue for enhanced hydrological modelling in northern Bénin. Actual evapo-transpiration is estimated using large aperture scintillometer equipment, devoted to sensible heat flux measurements. However, a previous study reported that the actual evapo-transpiration cycle is not fully understood. Indeed, the actual evapo-transpiration depends strongly on several factors such as climate, vegetation pattern, soil water storage and human activities. The respective contributions of the aquifer and vadose zone to the actual evapo-transpiration budget are not known. When using piezometric variations of the water table, the aquifer contribution is not easy to quantify since the specific yield may vary in the investigated area, located in a metamorphic rock environment. In the present study, we investigate whether significant differences in the aquifer's specific yield could exist within the large aperture scintillometer measurement area, leading to different actual evapo-transpiration water losses. We use joint frequency electromagnetic resistivity mapping, geological surveys and magnetic resonance sounding (MRS) to delineate the effective porosity of the regolith around the scintillometre measurement area. Thirteen MRS soundings implemented in key areas reveal a clear classification of the main geological units on the basis of their water content. The MRS water content varies between 1.5-3% for amphibolite and micaschists formations to more than 12% for quartzitic fractured formations, whereas the MRS relaxation time T1 is less discriminating (150-250 ms), indicating a small variation in pore size. Then, as a first modelling exercise, we assumed that the MRS water content (the effective porosity) maximizes the specific yield. The actual evapo-transpiration budget given by a previous study (Guyot et al. 2009) is then re-interpreted using geophysical data: we found that a) the measured water table depletion can explain the actual evapo-transpiration value providing enough water for the transpiration process and b) the significant discrepancies in actual evapo-transpiration signals observed between the eastern and western parts of the watershed can be explained by the respective effective porosity of the geological units. Even if further research is needed to link MRS water content to the specific yield and to evaluate a possible role of the deep vadose zone, the hydrogeophysical mapping presented in this study highlights the role of the MRS method for providing relevant information to understand hydrological processes in this complicated geological context of north Bénin.