Soil degradation is a major environmental problem in many parts of the world, including Slovenia. The spatially distributed WATEM/SEDEM model can be used to identify the most critical parts of the catchment with regard to soil erosion. Five Slovenian (Central Europe) catchments with inhomogeneous topography, land use, geological conditions, hydro-meteorological properties and sizes (catchment areas between 1 and 2000 km²) were modeled with calibrated parameters, while the WATEM/SEDEM model was calibrated with an automatic parameter estimation procedure, which is model independent. Both direct and indirect information regarding sediment yields, including turbidity measurements, daily suspended sediment concentration observations and bed load observations, were used for the WATEM/SEDEM model’s calibration. A detailed rainfall erosivity (R) factor map, which was constructed from 5-min rainfall data from 31 pluviographic meteorological stations, was used as one of the inputs for the WATEM/SEDEM model. The calculated mean annual soil loss was between 0.3 and 7.4 t/ha/year, and the sediment delivery ratio (SDR) ranged from 0.07 to 0.22 for 5 modeled catchments. The results indicate that the SDR decreases with increasing catchment area; however, the ratio between the average sediment yield and mean soil erosion obviously depends on many other factors, e.g., topography, climatic and geological conditions. The parcel trap efficiency parameter for forests had the greatest influence on the WATEM/SEDEM model’s outputs in all five case studies.