Extreme hydrological events can modify aquatic community structure resulting in significant changes in the ecosystem function. This study investigated the impacts of an extreme flood on the fish assemblage in the Gaobazhou reservoir, Yangtze River basin, which encountered devastating impacts of a severe flood in July 2016. The in situ effects of the severe flood on the fish assemblage were monitored by means of hydroacoustic surveys. Our study indicated that the flood had significant impacts on the fish assemblage in terms of fish density, biomass, structure, and distribution by modified hydrology. The fish density declined significantly (P < 0.05) from 3260 ind. ha(-1) in the pre-flood period to 431 ind. ha(-1) in the post-flood period, whilst the fish biomass increased from 237 to 526 kg ha(-1) due to escapees from cage culture that resulted from the flooding, respectively. The ratio of fish density in reservoir bays to mainstream in the post-flood period is 16.5 as opposed to 2.4 in the pre-flood period. Hydrological changes and escapees from cage culture resulting from flood had significant impacts on the modification of the fish assemblage in the reservoir.