The present water pollution situation at watershed level in China has been systematically analyzed. The causes of water pollution are attributed to the extensive economic developmental pattern, poor wastewater treatment, and a lack of nonpoint pollution control. The problems of water pollution control at watershed level include a lack of thought and approach, developmental delay in the environmental standard system, an inadequate monitoring ability, and an inefficient implementation of laws and regulations. From 2006 to 2020, water pollution control and governance will be a national key specific project of science and technology in China. The strategies of this project include establishing a water pollution control system at watershed level, orienting a healthy aquatic ecosystem, conducting risk management, and using comprehensive methods. The goal is to establish and complete a technological system of pollution control and management in three five-year phases. The main tasks are to develop common technologies, management systems, and mechanisms for lake eutrophication control, river pollution control, urban water environmental pollution control, potable water safety, and water environmental management. The bottlenecks of water pollution control and management in China could be systematically removed, and the demonstration of the system engineering approach will be conducted at selected key watersheds.