Conventional catchment-scale models are often calibrated using a single set of parameters and considering only statistical performance, overlooking hydrological aspects of great relevance for a realistic modeling outcome. The main objectives of this study were to set up a hydrological model in the Tagus River headwaters (Spain) with the new version of the soil and water assessment tool and to develop a novel calibration and evaluation procedure to simulate the hydrological processes realistically, particularly focusing on groundwater contribution. The model was parameterized at three geological regions, and its performance was evaluated in representative sub-catchments, addressing both soft and hard calibration to focus not only on daily streamflow but also on two hydrological indices: the runoff coefficient and the groundwater contribution. Results were then evaluated at the reservoir catchment level (two large reservoirs constitute the catchment outlet) and further validated on reservoir inflows. After this innovative procedure that incorporates a zonal calibration and a comprehensive model evaluation, a very good statistical performance was obtained, with NSE, R2, and PBIAS values (monthly) of 0.86%, 0.88%, and 2.5% for the Entrepeñas Reservoir inflows, and of 0.89%, 0.91%, and −8.5% for Buendía Reservoir. This performance was achieved while maintaining realistic values for the hydrological indices, providing a robust representation of the hydrological processes.