The Yangtze River, celebrated as the Mother River of the Chinese nation, constitutes a vital cradle of its civilization and a critical lifeline underpinning the nation's economic and social development. The high-quality development of the Yangtze River Economic Belt is fundamentally reliant on the superior ecological environment of its basin. Long-term, fixed-site observation of the basin's aquatic ecosystem provides the essential foundation for coordinating the protection and restoration of its water resources, water environment, and aquatic ecology. It is also of major scientific importance for advancing watershed aquatic ecosystem science and supporting the implementation of the national Yangtze River Conservation Strategy. This paper systematically reviews progress and experiences in the long-term fixed-site observation and experimental research on aquatic ecosystems within major river basins globally and in China. It outlines the developmental history and key achievements of long-term observational and experimental studies on the Yangtze River Basin's aquatic ecosystem. Furthermore, the paper summarizes the progress and outcomes realized since the initiation of the Joint Observation Research Initiative for Aquatic Ecosystem Security in the Yangtze River Basin (2023-2025). Supported by national field stations, this initiative has advanced the compilation of foundational datasets on the water ecological environment and the development of specialized technical standards for aquatic ecological observation. In response to the challenges confronting future long-term observation research in the Yangtze River Basin, this paper proposes forthcoming development trends and highlights priority areas requiring strengthening in subsequent fixed-site observation and experimental studies. This work provides a fundamental scientific basis for research and management decisions pertaining to the protection and restoration of the basin's aquatic ecosystem, while also offering a referential case for long-term in situ hydrological and ecological observation studies in large river basins worldwide.