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Canal plays a prominent role in improving regional transportation conditions, regional economic development and cultural dissemination. However, the complexity of the canal project will inevitably cause disturbance to water bodies and develop a series of impacts. This paper summarizes the engineering contents involved in the canal projects, combines the experience of the waterway and water conservancy hub on the water ecological environment, analyzes the main environmental impacts on the aquatic ecology along the canal during the construction and operation periods. Then effective countermeasures were proposed at different levels, such as canal design, engineering construction and ecological restoration. This work can serve as a reference for the protection of the aquatic ecological environment in canal development.