Territorial space planning has brought about a shift in the mindset of water ecosystem planning, placing high demands on the quality of water ecosystem planning. The implementation guarantee system of the planning is a crucial basis for ensuring the quality of plan. This paper aims to propose optimization suggestions for the implementation guarantee system of China’s water ecosystem planning, promoting the development of water ecosystem planning under the context of territorial space planning, and advancing the work of water ecosystem protection and restoration. Firstly, it summarizes the cross-border water ecosystem planning cooperation experiences in Europe, as well as the implementation guarantee system experiences of countries such as Germany, the Netherlands, and Singapore. Secondly, it reviews the exploration of domestic water ecosystem planning implementation guarantee. Then, after comparing domestic and international experiences and explorations, it is found that China’s water ecosystem planning system continues the “top-down” statutory planning approach, lacking legal integration across various fields, cross-regional and multi-departmental cooperation, and multi-channel environmental awareness promotion and public participation. Finally, the paper proposes optimization suggestions for the implementation guarantee system of China’s water ecosystem planning, focusing on aspects such as the transmission path of plan implementation, policy support measures, and public participation efficiency.