Magnetic resonance sounding (MRS) is a noninvasive geophysical method that allows estimating the free water content and transmissivity of aquifers. In this article, the ability of MRS to improve the reliability of a numerical groundwater model is assessed. Thirty-five sites were investigated by MRS over a ∼5000 km2 domain of the sedimentary Continental Terminal aquifer in SW Niger. Time domain electromagnetic soundings were jointly carried out to estimate the aquifer thickness. A groundwater model was previously built for this section of the aquifer and forced by the outputs from a distributed surface hydrology model, to simulate the observed long-term (1992 to 2003) rise in the water table. Uncertainty analysis had shown that independent estimates of the free water content and transmissivity values of the aquifer would facilitate cross-evaluation of the surface-water and groundwater models. MRS results indicate ranges for permeability (K = 1 × 10−5 to 3 × 10−4 m/s) and for free water content (w = 5% to 23% m3/m3) narrowed by two orders of magnitude (K) and by ∼50% (w), respectively, compared to the ranges of permeability and specific yield values previously considered. These shorter parameter ranges result in a reduction in the model's equifinality (whereby multiple combinations of model's parameters are able to represent the same observed piezometric levels), allowing a better constrained estimate to be derived for net aquifer recharge (∼22 mm/year).