This study investigates the robustness of the physically-based hydrological model WaSiM (water balance and flow simulation model) for simulating hydrological processes in two data sparse small-scale inland valley catchments (Bankandi-Loffing and Mebar) in Burkina Faso. An intensive instrumentation with two weather stations, three rain recorders, 43 piezometers, and one soil moisture station was part of the general effort to reduce the scarcity of hydrological data in West Africa. The data allowed us to successfully parameterize, calibrate (2014–2015), and validate (2016) WaSiM for the Bankandi-Loffing catchment. Good model performance concerning discharge in the calibration period (R2 = 0.91, NSE = 0.88, and KGE = 0.82) and validation period (R2 = 0.82, NSE = 0.77, and KGE = 0.57) was obtained. The soil moisture (R2 = 0.7, NSE = 0.7, and KGE = 0.8) and the groundwater table (R2 = 0.3, NSE = 0.2, and KGE = 0.5) were well simulated, although not explicitly calibrated. The spatial transposability of the model parameters from the Bankandi-Loffing model was investigated by applying the best parameter-set to the Mebar catchment without any recalibration. This resulted in good model performance in 2014–2015 (R2 = 0.93, NSE = 0.92, and KGE = 0.84) and in 2016 (R2 = 0.65, NSE = 0.64, and KGE = 0.59). This suggests that the parameter-set achieved in this study can be useful for modeling ungauged inland valley catchments in the region. The water balance shows that evaporation is more important than transpiration (76% and 24%, respectively, of evapotranspiration losses) and the surface flow is very sensitive to the observed high interannual variability of rainfall. Interflow dominates the uplands, but base flow is the major component of stream flow in inland valleys. This study provides useful information for the better management of soil and scarce water resources for smallholder farming in the area.