Abstract: Yueya Lake is one of main rivers in the main urban area of Nanjing City. Before the treatment, there were some problems, such as incomplete treatment of pollution sources, serious deterioration of water quality and damage of water ecosystem, which eventually made the water body black and stinky. To eliminate the black odor and improve the water quality, engineering and technical measures were implemented, including diversion of rainwater and sewage, endogenous treatment, construction of water ecosystem induced by Daphnia magna and “underwater forest”. The pollution source control, pollution interception, endogenous treatment and restoration of water ecosystem were carried out, and the management mechanisms were innovated, such as delicacy management, information supervision and strengthening public participation. The results showed that the water quality of Yueya Lake had been improved significantly with the main indicators such as ammonia nitrogen, total phosphorus and dissolved oxygen reaching Class Ⅳ standard of Surface Water Environmental Quality Standards (GB 3838-2002), and the water transparency increasing to more than 1 m. The water ecosystem of Yueya Lake had been restored, presenting a macrophytic lake, showing smooth drainage, clear water and green river bank and harmonious scene. To ensure water clean of Yueya Lake in the long period, the operation, maintenance and management of the system should be further strengthened, and the long-term management mechanism be implemented.