Water is an important link of material circulation and energy flow in ecosystem, and water ecosystem restoration plays a key role in regional ecosystem restoration. The severe human activities in Guangdong-Hong Kong-Macao Greater Bay area cause damage and interference to the river, lake and reservoir ecosystems, which causes serious pollution and reduction of aquatic organisms, leading to degradation or even loss of water ecological service function in the basin. Based on the scientific connotation of ecological restoration, it is judged that the health status of water ecosystem in the bay area has been under the threshold of non-biological control transition. In view of this situation, from the perspective of engineering construction, water environment treatment, spatial planning and management mechanism, this paper combs the recent works of water ecological civilization construction, water pollution prevention and control action plan, water ecological space delimitation and river management system related to water ecological restoration in the bay area, and organizes the technologies, indicators and systems used in them; then, it takes the comprehensive treatment of Maozhou River Basin and Wanlibidao in Guangdong Province as the water ecological restoration. based on the theory of ecosystem restoration and combining with the river, lake and reservoir ecosystem in Greater Bay Area, this paper puts forward a water ecosystem restoration framework suitable for the bay area, discusses the problems faced by water ecosystem restoration and prospects for future work, so as to provide a direct basis for water ecosystem restoration in the bay area.