To evaluate the disturbance caused by the tail reach project of the Ganjiang River on the river’s aquatic ecosystem, a two-year monitoring program was conducted on benthic macroinvertebrates within the main stem and its four downstream branches (the Main, North, Middle, and South branches). A total of 32 species belonging to 23 genera across 3 phyla were recorded. The ecological status was assessed using the benthic index of biotic integrity (B-IBI). The results indicated that the benthic community in the tail reach of the Ganjiang River was dominated by filter-feeding and pollution-tolerant mollusks. In terms of spatial distribution, the Main Branch and the slow-flowing areas upstream of the dam exhibited stable community structures and higher biodiversity. Conversely, the community compositions of the Middle, North, and South branches were relatively simple, characterized by lower biotic integrity. After the operation of the project, the Main Branch maintained the highest biotic integrity, demonstrating robust resistance to disturbance. Monitoring sites in the main stem, as well as the North and South branches, reached undisturbed or slightly disturbed status according to the B-IBI. However, the Middle Branch experienced significant shifts in community structure, indicating that its aquatic ecosystem was heavily disturbed by the project.