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The quantitative estimation of non-point source (NPS) pollution provides the scientific basis for sustainability in ecologically sensitive regions. This study combined the export coefficient model and Revised Universal Soil Loss Equation to estimate the NPS nitrogen (NPS-N) and NPS phosphorus (NPS-P) loads and then evaluated their relationship with Primary Industrial Output Value (PIOV) in the water source area of the middle route of South-to-North Water Diversion Project (SNWDP) for 2000–2015. The estimated results show that: (1) dissolved nitrogen (DN) load increased 0.55%, and dissolved phosphorus (DP) load decreased 4.60% during the 15 years. Annual loads of adsorbed nitrogen (AN) and adsorbed phosphorus (AP) increased significantly before 2005 and then decreased after 2005. Compared with 2000, AN and AP loads in 2015 significantly decreased by 32.72% and 30.81%, respectively. Hanzhong Basin and Ankang Basin are key areas for controlling dissolved pollution, and southern and northern regions are key areas for adsorbed pollution. (2) From 2000 to 2005, NPS pollutants and PIOV showed weak decoupling status. By 2015, NPS pollutants had strong decoupling from PIOV in most counties. (3) Land use has been the main source of NPS-N and NPS-P pollution, accounting for about 75% of NPS-N and 50% of NPS-P based on the average value over the study period. In the future, various measures—such as returning cropland to forest and reducing the number of livestock—could be adopted to reduce the risk of NPS pollution. NPS pollution caused by livestock was grown over the past 15 years and had not yet been effectively controlled, which still needs to be urgently addressed. Collecting ground monitoring data and revising parameters are effective means to improve the accuracy of simulation, which deserve further study. The results will also provide scientific support for sustainable development in similar regions.

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Temporal and Spatial Changes of Non-Point Source N and P and Its Decoupling from Agricultural Development in Water Source Area of Middle Route of the South-to-North Water Diversion Project