After decades of development, far-reaching progresses have been made in such aspects as water environment monitoring technology, basin water resources protection planning, environmental impact assessment for large- scale water project, and technical standard system in the scientific researches of water resources protection in the Yangtze River Basin. Supervision system, monitoring and control system, science and technology support system, as well as engineering system have been established for water resources protection. Despite the overall improvement of water environment in the Yangtze River Basin, local pollution is still outstanding, water security is insufficient,scientific support is inadequate,capacity construction lags,and regulatory means are weak,all far from the nation’s requirement for eco-civilization and environmental pollution as well as people’s demand for a better life. In view of this, we propose that scientific researches should be conducted based on the principle of great protection following the strategy of systematic protection and exploitation, and focusing on policies and safeguards, water-ecological civilization construction, control of total pollution into rivers, technical standard system, engineering system, as well as the introduction and application of new technologies.