Aquatic ecosystems are the basis for human survival. Due to climate change and human activities such as water resource exploitation, water pollution, overfishing and etc., aquatic ecosystems have been seriously damaged in recent years and the conservation and restoration of aquatic ecosystems have become a major challenge to the world. Scientific and reasonable assessments are the basic guarantee to achieve stable, healthy and sustainable management of aquatic ecosystems. Relevant management departments attach great importance to aquatic ecosystem assessments and have launched active exploration and practice. In this context, the development of aquatic ecosystem assessment and its definition and implications were thoroughly examined. The basic concepts and applications of the most widely used aquatic ecosystem assessment methods were sorted out and analyzed by the advantages and disadvantages. With a comprehensive understanding of aquatic ecosystem assessment methods, an aquatic ecosystem health assessment based on ecological integrity in basin management was proposed. Finally, the trends of aquatic ecosystem assessment are discussed. By discussing the theories, methods and trends of aquatic ecosystem assessment with researchers and managers in related fields, this paper aims to provide theoretical support for aquatic ecosystem assessment and management in China.