AbstractClimate change and human activities, for example, dam construction, largely affect hydrologic and hydrodynamic processes of river‐lake system, and hence exerted serious pressure on its aquatic ecology. It's challenging to restore its ecological environment without systematic investigation and knowledge about the features of hydrodynamics, water quality, and aquatic ecology. This study conducted field surveys of hydrodynamic, water quality, and fish distribution in the Yangtze‐Poyang system, the largest river and largest fresh lake in China, to investigate the effects of hydrologic and hydrodynamic variations on fish population dynamics, especially the extreme drought and its effects were largely concerned. In two surveys, discharge decreased from 12,000 m3/s to less than 1,000 m3/s. Distinct differences on fish density, species composition, and populations connectivity between two surveys were observed. During high‐water, connecting channel secured effective transition of river‐lake habitats, its strong hydrological connectivity and flow heterogeneity supported great biodiversity and bidirectional populations connectivity. Limited flow space and elevated turbidity during low‐water confined fish to a few channel units with sufficient depth and width, increasing fish density up to 7 times greater than during high‐water, and seriously weakening ecological connectivity of the system. Furthermore, species interaction was intensified due to limited environmental capacity, periodic strategists were favored while opportunistic strategists visibly diminished, leading to a dramatic decline in species by nearly half. In the future with increasingly frequent extreme climate, engineering measures, for example, effective ecological project regulation, are needful to alleviate the drought problem, being of great significance for maintaining ecological connectivity within the river‐lake system.