The Yangtze River, known as the Mother River of the Chinese nation, is a vital cradle of Chinese civilization and a core lifeline supporting China"s economic and social development. The high-quality development of the Yangtze River Economic Belt fundamentally depends on the excellent ecological environment of the Yangtze River Basin. Long-term fixed-site observation of the aquatic ecosystem in the Yangtze River Basin serves as the essential foundation for coordinating the protection and restoration of water resources, water environment, and aquatic ecology in the region. It also holds significant scientific importance for advancing the science of watershed aquatic ecosystems and supporting the implementation of the national strategy for Yangtze River conservation. This paper systematically reviews the progress and experiences in long-term fixed-site observation and experimental research on aquatic ecosystems in major river basins both domestically and internationally. It traces the development history and key achievements of long-term observation and experimental studies on the aquatic ecosystem in the Yangtze River Basin. Furthermore, it summarizes the progress and outcomes achieved since the launch of the Joint Observation Research Initiative for Aquatic Ecosystem Security in the Yangtze River Basin (2023–2025), supported by national field stations, particularly in terms of compiling fundamental datasets on the water ecological environment and developing specialized technical standards for aquatic ecological observation. Addressing the challenges and issues faced by future long-term observation research on the Yangtze River Basin"s aquatic ecosystem, this paper proposes development trends and highlights priority areas that require strengthening in future long-term fixed-site observation and experimental studies. The findings of this paper offer important guidance and practical value for ensuring the aquatic ecological security of the Yangtze River Basin and advancing the national strategy for its conservation.