<p>The Lake Chad Basin, located in the center of North Africa, is characterized by strong climate seasonality with a pronounced short annual precipitation period and high potential evapotranspiration. Groundwater is an essential source for drinking water supply as well as for agriculture and groundwater related ecosystems. Thus, assessment of groundwater recharge is very important although difficult, because of the strong effects of evaporation and transpiration as well as limited available data.</p> <p>A simple, generalized approach, which requires only a small number of field data, freely available remote sensing data as well as well-established concepts and models, is tested for assessing groundwater recharge in the southern part of the basin. This work uses the FAO-dual K<sub>c</sub> concept to estimate E and T coefficients at six locations that differ in soil texture, climate, and vegetation conditions. Measured values of soil water content and chloride concentrations along vertical soil profiles together with different scenarios for E and T partitioning and a Bayesian calibration approach are used to numerically simulate water flow and chloride transport. Average groundwater recharge rates and the associated model uncertainty at the six locations are assessed for the 2003–2016 time-period.</p> <p>Model results show that interannual variability of groundwater recharge is generally greater than the uncertainty of the modelled groundwater recharge. Furthermore, the soil moisture dynamics at all locations are limited rather by water availability for evaporation in the uppermost part of the soil and by water uptake in the root zone than by the reference evapotranspiration.</p>