The Ganjiang River has abundant fish resources, which plays a significant role in maintaining and replenishing the fish resources in Poyang Lake and the Yangtze River, and contains important habitat for migratory fish. However, fish diversity has rapidly declined in the Ganjiang River, especially migratory fish. In this study, 107 fish species (including 43 Chinese endemic species) were found in the middle and lower reaches of the Ganjiang River. However, only 91 fish species were found in the main channel of the Ganjiang River, which was lower than the 108 fish species historically found there. According to the Chinese Red List, 85 Least Concern, two Critically Endangered, three Vulnerable, one Near Threatened and 16 Data Deficient fish species were found in the Ganjiang River. In addition, the species number, diversity and CPUE in the channel were all greater than in the reservoir. The Bray-Curtis resemblance matrix and non-metric multidimensional scaling (NMDS) showed that the habitats of the Ganjiang River were divided into three areas. The analysis of RDA showed that turbidity, dissolved oxygen and water depth significantly affected fish distributions and assemblage composition. These results indicated that dam construction and other human activities have seriously destroyed the fish habitat and led to the decline in fish diversity. Therefore, the conservation of fish has become urgent in the Ganjiang River, and an integrated management plan should be developed and effectively implemented.