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Microorganisms in rivers indeed play a crucial role in nutrient cycling within aquatic ecosystems. Understanding the assembly mechanisms of bacterial communities in river networks is essential for predicting their special composition and functional characteristics in natural rivers. This study employed 16S rRNA gene amplicon sequence variation (ASVs) to scrutinize the bacterial community within the uniquely topographical Ili River network. The bacterial community composition varied across the three tributaries with distinct sources and the mainstream. The confluence of various sources diminished the diversity of the bacterial community and altered the functionality of within mainstream. We suggest that strong dispersal limitation predominantly shaped the community at the regional scale (46.6 %), underscoring the significant contribution of headwater sites to bacterial community composition. Contrary to expectation, the bacterial resources in the mainstream were not enriched by the higher diversity in three tributaries. Instead, confluence disturbance potentially increased the undominated processes (36.7 %) and alter the bacterial community composition at the local scale of the mainstream. The intricate coalescence at the confluence could potentially be an intriguing causative factor. Our research indicates that the composition of bacterial communities within intricate river networks exhibits biogeographic patterns, simultaneously influenced by river confluence and geographical features, necessitating multi-scale analysis.