This study investigates the hydrological dynamics of the Pativilca Basin in the Southern Hemisphere using the SWAT (Soil and Water Assessment Tool) model. Seventy-seven watersheds across a mountainous region were analyzed using elevation data, land cover, soil type, and gridded meteorological products (RAIN4PE and PISCO) for hydrological simulations. Watershed delineation, aided by a Digital Elevation Model, enabled the identification of critical drainage points and the definition of Hydrological Response Units (HRUs). The model calibration and validation, performed using the SWAT-CUP with the SUFI-2 algorithm, achieved Nash–Sutcliffe Efficiency (NSE) values of 0.69 and 0.72, respectively. Cluster analysis categorized the watersheds into six distinct groups with unique hydrological and climatic characteristics. The results showed significant spatial variability in the precipitation and temperature, with pronounced seasonality influencing the daily flow patterns. The higher-altitude watersheds exhibited greater soil water storage and more effective aquifer recharge, whereas the lower-altitude watersheds, despite receiving less precipitation, displayed higher flows due to runoff from the upstream areas. These findings emphasize the importance of incorporating seasonality and spatial variability into water resource planning in mountainous regions and demonstrate the SWAT model’s effectiveness in predicting hydrological responses in the Pativilca Basin, laying the groundwork for future research in mountain hydrology.