In the central part of the semi-arid Dargol Basin of southwestern Niger, most of the groundwater resource is contained in the fractured aquifers of the Precambrian basement. The groundwater resource is poorly characterized and this study is the first attempt to better describe the recharge mechanisms and hydrogeochemical behaviour of the aquifers. Hydrogeochemical and piezometric methods were combined to determine changes in recharge rate and origin of groundwaters for the shallow weathered aquifer and the deep fissured/fractured aquifer. At the basin scale, the groundwater fluxes towards the Niger River are influenced mainly by topography, with no visual long-term trend in groundwater levels (1980–2009). The hydro-geochemical signature is dominated by the calcic-bicarbonate to magnesian (70%) type. It shows evolution from an open environment with CO2 and low mineralized water (granitoids, alterites) towards a more confined environment with more mineralized waters (schists). Stable water isotopes (δ18O, δ2H) analysis suggests two main groundwater recharge mechanisms: (1) direct recharge with nearly no post-rainfall fractionation signature and (2) indirect recharge from evaporated surface waters and/or stream-channel beds. Groundwater tritium content indicates that recharge is mostly recent, with an age less than 50 years (3H > 3 TU), with only 10% indicating low or even no recharge for the past decades. A median value of the groundwater renewal rate estimated from individual values of tritium is equivalent to 1.3% year−1, close to the one determined for groundwater samples dating to the early 1980s, thus indicating no measurable long-term change.