Inland valleys are seasonally waterlogged headwater wetlands, widespread across West-Africa. Their role in the hydrological cycle in the humid, hard rock-dominated Sudanian area is not yet well understood. Thus, while in the region recurrent floods are a major issue, and hydropower has been recognized as an important development pathway, the scientific community lacks a precise knowledge of streamflow (Q) generation processes and how they could be affected by the presence of inland valleys. Furthermore, inland valleys carry an important agronomic potential, and with the strong demographic rates of the region, they are highly subjected to undergo land cover changes. We address both the questions of the hydrological functioning of inland valleys in the Sudanian area of West-Africa and the impact of land cover changes on these systems through deterministic sensitivity experiments using a physically-based critical zone model (ParFlow-CLM) applied on a synthetic catchment which comprises an inland valley. Model forcings are based on 20 years data from the AMMA-CATCH observation service and parameters are evaluated against multiple field data (Q, evapotranspiration – ET –, soil moisture, water table levels, and water storage). The hydrological model applied to the conceptual lithological/pedological model proposed in this study reproduces the main behaviors observed on a highly instrumented elementary catchment. We found that yearly water budgets were highly sensitive to the vegetation distribution: average yearly ET for a tree-covered catchment (944 mm) exceeds that of herbaceous-cover (791 mm). ET differences between the two covers vary between 12 and 24 % of the precipitation of the year for the wettest and driest year, respectively. As a consequence, the tree-covered catchment produces a yearly Q budget 28 % lower on average as compared to a herbaceous-covered catchment, ranging from 20 % for the wettest year to 47 % for a dry year. Trees also buffer interannual variability in ET by 26 %. On the other hand, pedological features (presence – or absence – of the low permeability layer commonly found below inland valley, upstream and lateral contributive areas) had limited impact on yearly water budgets but marked consequences on intraseasonal hydrological processes (sustained/unsustained baseflow in the dry season, catchment water storage redistribution ...). Therefore, subsurface features of inland valleys have potentially significant impacts on downstream water-dependent ecosystems and water uses as hydropower generation, and should focus our attention.