Inter-basin water transfer projects are designed to relieve water scarcity around the world. However, ecological problems relating to reductions in protection zone functions can occur during inter-basin transfers. This paper uses the largest inter-basin water transfer project in the world, namely, the South-to-North Water Transfer Project (SNWTP) in China, as an example to analyze the variation of Miyun Reservoir’s inner protection zone functions when water is transferred. Specifically, a riparian model (RIPAM) coupled with remote sensing data were used to calculate the nitrogen (N) and phosphorus (P) losses due to plant uptake, and these results were validated by in situ survey data. Then, correlations between water levels and N and P removal were analyzed. The results show that water table disturbances resulting from elevated water levels strongly influence the growth of plants and have obvious negative impacts on N and P removal in the inner protection zone. With the implementation of the middle route of the SNWTP, the water level of Miyun will rise to 150 m in 2020, and subsequently, the total net primary productivity (NPP) could decline by more than 40.90% from the level in 2015, while the N and P uptake could decline by more than 53.03% and 43.49%, respectively, from the levels in 2015, according to the modeling results. This will lead to declines in the inner protection zone’s defense effectiveness for N and P interception and increases in risks to the security of water resources. The results of this study provide useful knowledge for managing the defense function of the terminal reservoir’s inner protection zone and for ensuring that water quality is maintained during the diversion process.
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