Land use conversion from rainfed to irrigated cropping increases drainage and groundwater recharge, yet reliable estimates of the magnitude of the change are difficult to obtain for shallow aquifers. In the semiarid Komadugu Yobe River valley (Lake Chad basin, SE Niger), the area of irrigated cropping has doubled in the last three decades, which may have increased recharge fluxes to the shallow (∼6 m in depth) water table. To quantify the increase in recharge, water flow in the vadose zone was modeled, taking into account the predetermined heterogeneity of the River alluvium. For each sedimentary unit, soil moisture was monitored in situ under controlled hydraulic surface conditions by vertical neutron probe surveys. Using one-dimensional numerical simulations in a Monte-Carlo procedure, probability density functions (PDFs) of soil hydraulic parameters that reproduce moisture measurements were established. The centers of the PDFs were shown to be in accordance with the textural classification inferred from grain size analyses. The PDFs were then combined with a three-dimensional geological model of the alluvium and the groundwater recharge was simulated separately under irrigated and rainfed cropping conditions. The results showed that the uncertainty in soil hydraulic parameters (i) strongly influenced the absolute values of the simulated recharge, but (ii) only slightly affected the simulated differential recharge between irrigated and rainfed cropping conditions. The increase in groundwater recharge was therefore well constrained and was estimated at 15 cm (dry year) and 25 cm (wet year), i.e., representing 18 and 23% of water input. The approach described here is applicable to most shallow aquifers in River valleys where surface water is used for irrigation, a widespread characteristic of semiarid regions.