Nitrogen and carbon are important elements regulating the structure and function of river ecosystems; therefore, determining their sources has important implications for integrated river basin management. Since physical processes and human activities can lead to different isotopic signatures in organic matter, the characteristics of the stable isotopes of carbon and nitrogen could be used to determine carbon and nitrogen sources in riverine systems. The upper Han River is the water source area for the Middle Route of the South-to-North Water Diversion Project (MR-SNWTP); hence, identifying pollutant origins in the riverine system is critically important for the interbasin water transfer project. In this study, we investigated the δ¹³C and δ¹⁵N values of particulate organic matter (POM) and δ¹⁵N values of nitrogen including nitrate-nitrogen (N-NO₃^-) and ammonium nitrogen (N-NH₄⁺) to trace the sources of organic matter in the river ecosystem. The study site was the Jinshui River with a length of 87 km and drainage area of 730 km² in the upper Han River during 2012-2013. Furthermore, we measured chlorophyll content, turbidity, and the concentrations of N-NH₄⁺ and N-NO₃^- in the river system using YSI 6920. The results demonstrated spatial variability in POM, with higher content in the moderately disturbed zone and intensely disturbed zone than in the slightly disturbed zone. The concentration of ammonium showed seasonality with minimal concentrations (0.07 mg/L) in the spring and maximum concentrations (0.45 mg/L) in winter, whereas the maximum concentration of nitrate was 0.44 mg/L in winter and the minimal value was 0.08 mg/L in summer. The carbon isotope value of POM also showed an obvious seasonality, in decreasing order of spring, summer, winter, and fall. The turbidity reached its maximum in summer from the heavily rainfall in the same season due to the monsoon climate. The Chl/turbidity ratio could be used to identify the contribution of algae to the total particulate organic materials in the river. Algae, which have a higher carbon isotope value (-21.18‰——27.14‰) than terrestrial organic matter (-27.34‰——28.83‰), were the main source of POM. POM with an N isotope range of -8.03‰-14.5‰ primarily originated from soil organic matter and plankton. The dissolved nitrate with isotope ranges of -5.86‰ -17.20‰ for ammonium and -1.48‰-15.86‰ for nitrogen in the riverine system primarily originated from precipitation, plankton, and fertilizer. Also, larger values for δ¹⁵N-NH₄⁺ and δ¹⁵N-NO₃^- were observed in the growing season (i.e., spring/summer), which was possibly due to the seasonally higher chlorophyll concentration (i.e., high algae density in the river). Additionally, the low nitrate stable isotope value and low concentration of ammonium and nitrate in summer were possibly due to nitrification and alga uptake in the riverine system. Moreover, microbial denitrification could increase the nitrate stable isotope value and decrease nitrate concentrations; our results showed that the maximum δ¹⁵N value appeared in winter due to the low temperatures. The research implies that N-loading from the catchment reflects the upland land use pattern along the riverine system, and the isotopic technique could be an effective approach for quantifying pollutant sources in river systems.