Soil in riparian zone can alleviate the risk of nitrogen pollution for water by releasing gaseous nitrogen (N) fluxes. As a critically terminal riparian zone in China, the Miyun Reservoir riparian zone is dramatically submerged by water delivered by the South-to-North Water Transfer Project (SNWTP), which is the largest inter-basin water transfer scheme worldwide. However, few studies have proposed a framework to estimate the effect of SNWTP on N removal by soil at the scale of the riparian catchment. Therefore, a framework that integrates the eco-hydrological model, remote sensing technology, and scenario setting was developed in this study to simulate the spatiotemporal variation of N emissions and to estimate the influences of SNWTP on N removal by soil in the Miyun riparian catchment between April and September of 2015. The simulated results indicate that N removal in the whole catchment ranged from 48.83 t to 290.58 t between April and September and the total N removal was 871.97 t in 2015. With water level exceeding 150 m and 160 m, the riparian soil had about 35%-60% of its original N pollution mitigation ability. Changing farmland and grassland into forestland can effectively offset the impacts of SNWTP.