Knowledge about the ecological patterns of abundant and rare bacteria in regulated river ecosystems, especially with respect to their community traits, is an important but poorly investigated subject. In this study, we examined the community assembly of abundant and rare bacteria, as well as their environmental adaptation, across complex environmental gradients in sediments of the Yarlung Tsangpo River on the Tibetan Plateau. Results showed that abundant taxa exhibited broader environmental thresholds and stronger phylogenetic signals for ecological traits than rare taxa. In contrast, rare taxa were more sensitive to environmental changes and showed stronger phylogenetic clustering. Although both subcommunities exhibited significant distance-decay patterns, the abundant subcommunity was governed primarily by dispersal limitation, while the rare subcommunity was strongly driven by heterogeneous selection. The similar distribution patterns but contrasting assembly mechanisms affecting abundant and rare subcommunities resulted from the differences in environmental adaptation. Forest area and total nitrogen were key factors in determining the stochastic and deterministic assembly for abundant and rare subcommunities, respectively. Additionally, rare taxa might play potential roles in maintaining network stability, although they were less connected and located more peripherally within the network. Collectively, our study provides a new perspective for the ecological significance of abundant and rare bacteria in fluvial sediments, and facilitates the prediction of microbial responses to ongoing environmental changes in the Yarlung Tsangpo River.