The assessment of soil erosion rate, especially in agricultural lands, represents a fundamental tool for land management planning in the long-term period. In this study, the SWAT model was utilized to simulate soil erosion within a semi-arid watershed in South Portugal. The model was successfully calibrated and validated using real data of streamflow and river sediment transport in four hydrometric stations. Soil erosion susceptibility maps (historical and future) were realized to highlight the evolution of the phenomenon through time. The historical period was confirmed to be the worst one in terms of average soil erosion for each land use, followed by the Representative Concentration Pathways (RCPs) 8.5 and 4.5 scenarios. The main differences in soil loss among the two RCPs will be influenced by the slightly increasing trend of extreme events which will characterize the RCP 8.5, leading to a higher maximum value of soil erosion. Results highlighted the tendency to erosion of Leptosols and of the agro-forestry system (“montado”), which influenced the soil erosion susceptibility distribution of the whole basin. The study confirmed that Leptosols are the most subject to sediment loss due to their intrinsic characteristics, and that “montado” and farmed systems will negatively influence soil erosion rate if anti-erosion actions will not be adopted, stressing the need to identify all aspects responsible for land degradation in Mediterranean watersheds.