Abstract: Cross-basin water transfer solves the spatial imbalance of water resources between river basins. However, water transfer may introduce water bodies of different properties into the receiving area, which has an impact on the water quality and water ecology of the local water bodies. The existing studies mostly focused on the impact of water diversion on the upstream ecological environment, but little attention was paid to the impact on the nutrient and organic comprehensive indicators of downstream lake-type reservoirs. Miyun Reservoir, as a lake-type reservoir, is Beijing's surface drinking water source and strategic water reserve base. The impact of the South-to-North Water Diversion Project on its water quality is of particular concern. Based on the primary water quality monitoring data, this study took September 2012 (before water transfer), September 2015 (the start of water transfer), and September 2018 (after water transfer) as the time nodes, and analyzed the quantitative impact of cross basin water transfer on the nutrient and organic comprehensive indicators in Miyun Reservoir. The comparative analysis method was used in this paper. The results showed that the influence of cross basin water transfer on Miyun Reservoir was related to the local water depth. After the operation of the South Water Diversion, the total phosphorus in the deep water area increased by 8.2%, compared to the previous one, which was higher than that in shallow water areas; The total nitrogen showed a downward trend, and the decrease in deep water area was lower than that in the shallow water area. Water transfer enhanced the physical, chemical, and biological activities of water bodies in shallow water areas, and aggravated the pollution trend of reducing organic and inorganic substances in shallow water areas. The concentration of pollutants was found to increase by 34.9%, compared to that in the previous year. After the operation of the Southern Water Transfer, the concentration of chlorophyll in shallow water areas increased by 18.9%, compared to the previous month, and consequently resulted in an increased trend of eutrophication, which was more significant than that in deep water areas.