Now more and more ecologists concern about the impacts of dam construction on fish. However, studies of fishes downstream Gezhouba Dam were rarely reported except Chinese sturgeon (Acipenser sinensis Gray). In this study, catch investigations and five hydroacoustic detections were completed from 2015 to 2016 to understand the distribution, size, and categories of fishes and their relationship with the environmental factors below Gezhouba Dam in protected reach in the Yangtze River main stream. Results showed significant differences in fish distribution and TS (target strength) between wet and flood seasons. Mean TS in five hydroacoustic detections were −59.98 dB, −54.70 dB, −56.16 dB, −57.90 dB, and −59.17 dB, respectively, and dominant fish species are Coreius guichenoti (Bleeker), Siniperca chuatsi (Basilewsky), and Pelteobagrus vachelli (Richardson). In the longitudinal direction, fish preferred to stay in some specific sections like reaches 2, 4, 7, 8, 11, and 16. Since hydrology factors change greatly in different seasons, environmental characteristics vary along the reaches, and human activities play an important role in the fish behavior, it is concluded that great cross-season changes in hydrology lead to the differences in TS and fish assemblages and that geography characteristics, especially channel geography, together with human activities influence fish longitudinal distribution. This finding provides basic knowledge of spatiotemporal distribution and assemblages of fishes in the extended reaches downstream Gezhouba Dam. In addition, it offers implications for river management. It could also serve as reference of future research on fish habitat.