<p>Unimpeded river flow is indispensable for species migration, yet dam constructions disrupt this process. Although river discontinuity has been studied across a dam, a comprehension of the ecological fragmentation caused by the reservoir backwaters behind a dam remains constrained. This study assessed the beta diversity, including taxonomy, dispersal traits, and phylogenetics, and analyzed their relationship with environmental and geographical distance in the Three Gorges Reservoir of southern China. The reservoir studied was divided longitudinally into three sections: stable backwater, fluctuating backwater, and an intercross section in between. The distance-decay effect was found most pronounced in the intercross section, illustrating how hydrological fragmentation between the backwaters causes ecological barriers along the reservoir of a dam. Furthermore, beta diversity of the species within a functional group characterized by the hydrochory dispersal trait was found a strong link to the distance-decay effect in the backwater intercross, pointing to the dispersal limitation of hydrochory is intensified. Our research emphasizes the importance of addressing the dispersal limitations of plant propagules arising from the fragmentation of flow patterns caused by the dam-induced different backwaters. This highlights the urgent need to enhance connectivity between the backwaters to mitigate ecological barriers, thereby aiding in the restoration of riverbanks.</p>