In Burkina Faso, the basement aquifers represent a major asset in terms of quantity and quality, for both drinking and irrigation purposes for rural populations. They provide water resources that can guarantee the long-term needs of the populations, provided that a sustainable management policy for these resources is adopted. Yet, any groundwater resource management policy is necessarily linked to a better knowledge of aquifer recharge mechanisms, which is yet to be fully assessed in the Sahelian basement area. The objective of this study was to characterize the recharge mechanism within the experimental site of Sanon, located in the basement zone in Burkina Faso, using a coupling of hydrodynamic and chemical approaches. The hydrodynamic approach consisted of monitoring the spatial and temporal distribution of the piezometric levels of the aquifers along a north–south and east–west transect and determining soil infiltration capacity. The hydrochemical characterization of the aquifers was carried out through an analysis of groundwater samples from the concerned aquifers and daily tracing of the electrical conductivity of the aquifer water. The cross-analysis from the results of the implemented approaches shows a direct recharge mechanism through rainwater infiltration in the central valley, an indirect recharge mechanism in the lowlands, and a recharge mechanism by lateral transfers in the peripheral aquifers of the Sanon experimental catchment. The existence of a piezometric dome reveals in the central valley a zone of preferential recharge and water movement. The water of the central valley is the least mineralized with electrical conductivities below 100 µS/cm. This mineralization follows the direction of the water flow.