Abstract: The Chao-Bai River Basin, a vital water source area in North China and a representative agricultural-urban coupled ecosystem, faces severe challenges to regional water security and ecological health owing to nitrate pollution in its surface waters. This study focused on the upper reaches of the Chao-Bai River Basin. Surface water samples were collected across different land uses in differen river sections during the dry season (February and April) and wet season (July) of 2022. A combination of hydrochemistry, nitrogen and oxygen isotopes, and the SIAR Bayesian mixing model was used to evaluate nitrate sources and transformation processes, revealing the changing trends of nitrate pollution sources under the influence of different timescales and land-use types. The results showed significant spatial and temporal differences in nitrate concentrations. In February, the highest average nitrate concentrations were in the study area, with 48.5 mg∙L⁻¹ in the Chao River and 25.7 mg∙L⁻¹ in the Bai River. In April, nitrate concentrations declined owing 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. River sections influenced by agricultural activities exhibited greater variability in nitrate concentrations than those influenced by forested areas, highlighting the substantial impact of farming activities on water quality. The SIAR model showed that major nitrate sources were precipitation and soil nitrogen (55.3%−86.7%), domestic sewage/manure (10.2%−28.7%), and chemical fertilizers (3.1%−18.9%). During the rainy season, domestic sewage/manure and chemical fertilizer inputs increased by approximately 1-fold and 3−6 fold compared with the dry season. Nevertheless, domestic sewage/manure contributions remained higher than fertilizers. Spatially, the Bai River Basin, characterized by intensive agricultural land, exhibited a greater reduction in fertilizer-derived nitrate contributions from February to April than the contemporaneous Chao River Basin, alongside a larger increase in domestic sewage and manure input during the same period. This suggests stronger nitrogen leaching capacity from farmland in the Bai River watershed than that in the Chao River watershed. This study systematically elucidated the underlying mechanisms controlling nitrate distribution patterns and source variations in surface waters across different river sections of the upper reaches of the Chao-Bai River Basin and revealed their complex interactions with natural hydrological processes and anthropogenic activities. This study provides a basis for the analysis of nitrate sources and pollution control in the Chao-Bai River Basin and rivers in other semi-humid to semi-arid regions. These findings also provide a scientific foundation for controlling agricultural non-point source pollution and promoting sustainable watershed development in the Beijing-Tianjin-Hebei region.