Abstract: The Chao-Bai River Basin, serving as a crucial water source area in the North China and a typical agricultural-urban coupled ecosystem, faces severe challenges to regional water security and ecological health due to nitrate pollution in its surface waters. This study focuses on the upper reaches of the Chao-Bai River Basin. Surface water samples were collected from different land-uses during the dry season (February and April) and the wet season (July) of 2022. The combined use of hydrochemistry, nitrogen and oxygen isotopes, and the SIAR Bayesian mixing model were used to evaluate nitrate sources and transformation processes, revealing the changing trends of nitrate pollution sources under the influence of different time scales and land use types. First, the results showed that there were significant spatial and temporal differences in nitrate concentrations. In February, the highest average nitrate concentrations were in the Chao-Bai River, with 48.5 mg/L in the Chao River and 25.7 mg/L in the Bai River. In April, nitrate concentrations declined due to assimilation by algae and aquatic plants. In July, elevated nitrate concentrations in the Bai River resulted from non-point source pollution from tributaries during the rainy season. The river sections dominated by agricultural activities demonstrated significantly higher variability in nitrate concentrations compared to those in in forested areas, highlighting the substantial impact of farming activities on water quality. Second, the SIAR model showed that main nitrate sources were precipitation and soil nitrogen, domestic sewage/manure, and chemical fertilizers, which contribution rates were 55.3%−86.7%, 10.2%−28.8%. and 3.1%−18.7%, respectively. During the rainy season, precipitation-driven nitrogen leaching increased domestic sewage/manure and fertilizer inputs by approximately 2-fold and 3−6 fold compared to the dry season, respectively. Nevertheless, domestic sewage/manure contributions (12.6%−28.8%) remained significantly higher than fertilizers (9.9%−18.9%). At the spatial scale, the Bai River Basin, which is predominantly agricultural land, exhibited greater reductions in fertilizer-derived nitrate contributions from February to April compared to the contemporaneous Chao River Basin, while showing a greater increase in domestic sewage and manure inputs during the same period. This spatial pattern indicates stronger nitrogen leaching capacity from farmland in the Bai River watershed than in the Chao River watershed. The study systematically elucidates the underlying mechanisms controlling nitrate distribution patterns and source variations in surface waters across different reaches of the Chao-Bai River Basin, revealing their complex interactions with natural hydrological processes and anthropogenic activities. To provide a basis for the analysis of nitrate sources and pollution control in Chao-Bai River Basin and even rivers in other semi humid to semi-arid regions. These findings also provide a scientific foundation for managing agricultural non-point source pollution and promoting sustainable watershed development in the Beijing-Tianjin-Hebei region.