As a critical ecological barrier and core water conservation zone in China, the southern slope of the Qinling Mountains plays a pivotal role in safeguarding regional ecological security and ensuring a safe drinking water supply, largely mediated by groundwater quality. However, systematic investigations into nitrate contamination in this region remain limited, and the dominant sources as well as hydrogeochemical migration pathways of nitrate are still poorly constrained. To address these knowledge gaps, this study targets representative watersheds on the southern slope of the Qinling Mountains, with an emphasis on characterizing the spatial – temporal distribution patterns and identifying the primary sources of groundwater nitrate. A multi-gradient monitoring network was established along the Han River and its tributaries, supporting seasonal sampling across both dry and wet periods. Coupled with δ15N-δ18O dual-isotope tracing and comprehensive regional environmental background surveys, we quantitatively assessed the spatial heterogeneity, temporal dynamics, and source apportionment of nitrate in groundwater. Results reveal pronounced spatial variability: mean nitrate concentrations decrease downstream, and levels adjacent to the main stem are consistently lower than those in tributary zones. Furthermore, the spatial distribution of nitrate closely parallels the regional groundwater flow direction. Vertically, soil nitrate concentrations decline with depth overall, yet exhibit anomalous enrichment at a depth of ~1 m ‒ indicating that nitrate leaching has penetrated to at least this depth. Source apportionment indicates that soil nitrogen, livestock and poultry manure, and domestic sewage collectively account for the majority of nitrate inputs to groundwater. This study provides foundational observational data on groundwater nitrogen cycling in mountain – basin transitional zones, thereby strengthening the scientific basis for groundwater protection and ecosystem management in the region. It also advances theoretical understanding of nitrogen biogeochemistry in complex terrain and supports the development of targeted, evidence-based groundwater pollution mitigation strategies.