Abstract: As an important drinking water source to north China, the Middle Route of the South-to-North Water Diversion Project (SNWDP) requires very high water quality protection. At the planning and design stage of the project, the influence of precipitation and dust along the channel, polluted runoff from the bridge deck, storm flood risk and accident capsizing on the channel water quality were taken into account. According to the design requirements of the environment impact assessment report (EIA), a systematic water quality assurance system was established in SNWDP, which ensures water quality in class I and II stably after water supply (total nitrogen is not evaluated). The monitoring results have showed that some water quality indexes increased along the route after the main channel was flooded. In the early stage of water supply, excessive algae proliferation occurred. Factors such as atmospheric dry and wet deposition, bridge surface runoff, stormwater overflow and groundwater discharge may cause pollution input. The variation of hydrochemical process driven by factors such as the temperature difference between north and south and the season, the gradient of pH value may be the important factors influencing the change of water quality. The material circulation of the channel ecosystem is interlaced and coupled with various factors such as water flow process, habitat evolution and biological community evolution, which may be an important mechanism driving the spatio-temporal variation of water quality indexes related to the source factors of ammonia nitrogen, total nitrogen and total phosphorus. Due to the lack of understanding the complexity and huge system of main channel, it is difficult to predict the change of water quality. It is suggested that the long-term water quality guarantee of the main channel should focus on solving the problems of system cognition, simulation and prediction, regulation and management.