Water environment management is the inevitable requirement of ecological civilization construction. With the rapid development of economy, the discharge of all kinds of pollutants increases, and the water environment problems in Yancheng become increasingly prominent. In recent years, Yancheng City has actively carried out water environment management, and the water quality has improved year by year, and the discharge of major pollutants has decreased year by year. However, due to the short time for comprehensive water environment management, there are still some problems in practice, such as relatively traditional management mode and measures, little help and support from science and technology, low level of capital and talents, insufficient ecological restoration capacity, and unstable governance effect. Therefore, combined with the actual situation of Yancheng City, this paper puts forward countermeasures and suggestions for water environment management based on the concept of ecological civilization, including mobilizing multiple subjects to participate, innovating watershed governance mode, strengthening scientific and technological information support, strengthening capital and talent guarantee, rationally determining water treatment plans, promoting ecological protection and restoration of rivers and lakes, improving environmental infrastructure, and deeply implementing the river chief system. The purpose is to provide reference for Yancheng to practice the concept of ecological civilization and carry out water environment governance in the new era.