Abstract: Accurate identification and quantification of non-point source (NPS) pollution fluxes entering rivers is a critical scientific step for precise prevention and control of agricultural NPS pollution. Current research and practices primarily focus on process simulation at the watershed scale from source to sink, yet lack direct quantitative methods to trace pollution backward from sink to source based on cross-sectional monitoring data. Taking the Ciba section of the Linjiang River in Yongchuan, Chongqing City, as a case study, we calculated total pollutant fluxes using high-frequency water quality and flow monitoring data. By applying hydrological flow separation techniques and wastewater treatment plant discharge fluxes, we estimated baseflow pollution fluxes and point-source pollution fluxes, and calculated surface runoff NPS pollution fluxes and their contribution rates. The results showed that the interannual difference in pollutant fluxes at the Ciba section was significant from 2021 to 2024. NH₃-N flux increased with annual precipitation and peaked in 2021, while summer saw the highest nitrogen and phosphorus fluxes overall. However, peak TN and TP fluxes occurred in 2022, a year with relatively low annual precipitation. Since spring precipitation accounted for 57% of the total for that year, concentrated rainfall coincided with spring farming and fertilizer application, intensifying surface erosion and nitrogen and phosphorus loss, thus making 2022 the only year dominated by spring-time NPS pollution. The Eckhardt method provided the best hydrological fitting results, with baseflow contributing 4.1%-9.1% to total pollution fluxes and point sources contributing 14.7%-36.3%. The NPS contributions for NH₃-N, TN, and TP fluxes were 73.5%-79.7%, 80.3%-81.3%, and 56.3%-56.5%, respectively. NH₃-N NPS fluxes were concentrated mainly in summer, while TN and TP contributions were primarily concentrated in summer and autumn, with TN consistently showing higher NPS proportions. This study provides a highly operational methodology and practical case support for load assessment, precise identification, and responsibility attribution of NPS pollution in water environment management.