Abstract: In recent years, geographic information system (GIS) and remote sensing system (RS) (2S technology) have been widely used in the fields of hydrology and water environment. However, in the current water ecology research, how to scientifically analyze and diagnose the large-scale spatio-temporal ecological degradation of watershed is still a difficult problem. Considering the needs of quality management of water ecology and the spatiotemporal diagnosis of aquatic organisms in China, this paper comprehensively investigates the research progress in the application of 2S technology in aquatic organisms at home and abroad in the past 20 years, and expounds its applicability, advantages and disadvantages. The results show that in recent years, the main achievements of 2S technology in the spatio-temporal analysis of aquatic organisms have increased significantly, especially in the fields of aquatic plants and chlorophyll. In the spatio-temporal analysis of aquatic organisms in the watershed, the most popular methods of GIS technology are buffer zone analysis, overlay analysis and spatial interpolation, which can delimit buffer zone, calculate the spatio-temporal information of aquatic organisms and analyze the spatio-temporal trend of aquatic organisms. RS technology can rapidly acquire long-term data of aquatic organisms through empirical, semi-empirical and mechanism analytical models, which can spatially simulate and trace back the source of aquatic organisms. The application of 2S technology is an important and promising tool for spatio-temporal analysis of aquatic organisms in large-scale, which can better identify the spatio-temporal variation and the reasons of degeneration of aquatic organisms in the watershed. As for the future diagnosis of spatio-temporal problems of water ecological in large-scale, it is a significant direction to develop intelligent monitoring equipment, such as automatic monitoring and rapid identification of aquatic organisms, and integrate 5G technology, big data analysis, cloud computing, AI and 2S technology.