Climate anomalies such as drought may lead to cascading effects on river ecosystems, ultimately resulting in the change of aquatic biocenosis. Here, we investigated functional assemblies of fish communities at three sites below the Gezhouba Dam of the middle Yangtze River in China before and during a drought event from 2021 to 2022. As the drought proceeded, the richness of the fish functional groups decreased, and the abundance of demersal/invertivore species increased. These changes might indicate adaptive responses of fish communities to the reduction in water volume and shrinkage in habitat areas. The shifts in functional structure also caused fish communities to become more similar during the drought. The null model based on functional traits showed a distance effect of the fish community assembly rules. The communities close to the dam were structured more stochastically under drought stress, which may be attributed to the impact of ecological operation by cascade hydro-junctions. In contrast, the communities far away from the dam were structured by environmental filtering. Our results support the hypothesis that the natural hydrological regime is the main force driving the spatiotemporal dynamic of riverine fish assemblages, and the drought stress on fish communities may need more attention to cope with future biodiversity loss under global climate changes.