Achieving sustainable agricultural intensification in inland valleys while limiting the impacts on water quantity and water quality requires a better understanding of the valleys’ hydrological behavior with respect to their contributing watersheds. This study aims at assessing the dynamics of hydrological processes and nitrate loads within inland valleys that are experiencing different land uses. To achieve this goal, an HRU-based interface (ArcSWAT2012) and a grid-based setup (SWATgrid) of the Soil Water Assessment Tool (SWAT) model were applied to three headwater inland valley watersheds located in the commune of Djougou in central Benin that are characterized by different proportions of cultivated area. Satisfactory model performance was obtained from the calibration and validation of daily discharges with the values of R2 and NSE mostly higher than 0.5, but not for nitrate loads. The annual water balance reveals that more than 60% of precipitation water is lost to evapotranspiration at all sites, amounting to 868 mm in Kounga, 741 mm in Tossahou, and 645 mm in Kpandouga. Percolation (302 mm) is important in the Kpandouga watershed which is dominated by natural vegetation at 99.7%, whereas surface runoff (105 mm) and lateral flow (92 mm) are the highest in the Kounga watershed having the highest proportion of agricultural land use (14%). In all the studied watersheds, nitrate loads are very low (not exceeding 4000 KgN per year) due to the low fertilizer application rates, and the water quality is not threatened if a standard threshold of 10 mg/l NO3-N is applied. The results achieved in this study show that SWAT can successfully be used in spatial planning for sustainable agricultural development with limited environmental impact on water resources in inland valley landscapes.