This study aims to evaluate the suitability of the Soil and Water Assessment Tool model in simulating runoff and sediment loss in the Carapelle (SE Italy), a typical Mediterranean watershed, where continuous measurements of streamflow and sediment concentration were collected over a 5‐year period, on a half‐hour timescale, processed on a daily timescale. After sensitivity analysis, the model was calibrated and validated for runoff and sediment. Statistics show generally satisfactory efficiency. To further improve sediment simulation performance, we used a seasonal calibration scheme, in which data recorded in the dry and wet seasons were used to calibrate sediments separately, on a seasonal basis. We also tested the model's capability in identifying the major sediment source zones and river segments where there is sediment deposition. On the basin scale, the average water yield (186 mm) corresponds to 27% of the total rainfall (686 mm), and average annual sediment load was estimated to be 6.8 t ha−1 year−1. On the subbasin scale, a gradient of sediment yield was found that is characterised by a large difference among the upper (7 to 13 t ha−1 year−1), central, and lower parts (<1 t ha−1 year−1) of the study area. Conversely, deposition in channel flow has its highest values in the central part of the watershed, where there is an alluvial plain. Winter wheat and olive land use are the major source areas, in terms of sediment. This study confirms that the Mediterranean watershed is a fragile ecosystem, and measures are needed to mitigate soil depletion.