Intensive agriculture in semi-arid watersheds is considered a threat to global water security; however, the hydro-agronomic mechanisms that control diffuse pollution sources are often insufficiently characterized at the watershed scale. This study evaluates the hydrological response and nitrate leaching dynamics in the Upper Aguascalientes watershed by implementing the SWAT model, forced with meteorological data and calibrated using runoff derived from ERA5 reanalysis. Methodologically, the Potential Nitrate Leaching Risk Index (IRP_N) was formulated and coupled to the hydrological results. The comparative analysis shows that ERA captures the temporal dynamics of the HRUs, although it tends to significantly overestimate runoff volumes. The basin exhibits a marked scale-dependent duality, with the upper zone operating under a Hortonian regime, while the lower basin exhibits attenuation at the basin scale due to spatial integration and distributed storage processes. The $\left(IR{P}_N\right)$ analysis demonstrates a critical disconnect between fertilization rates (>1300 kg N·ha⁻¹) and crop absorption capacity, turning excess nitrogen into a rapid transport vector during runoff events. Finally, the results underscore the need to complement water management and infrastructure strategies with technical training programs and regulatory frameworks that promote modern agricultural practices aligned with the system’s retention capacity.