Bacterioplankton are an important part of freshwater ecosystems such as rivers. To explore the seasonal dynamics and driving mechanisms of bacterioplankton communities in the river of the southeastern Himalayan basin, we used 16S rRNA high-throughput sequencing technology to analyze the diversity, biogeographical patterns and driving factors of bacterioplankton communities at 33 different sites in the river of the southeastern Himalayan basin in terms of time scale in spring (May), summer (July) and autumn (September). The results showed that: (1) Proteobacteria, Actinobacteriota, Bacteroidota and Cyanobacteria were the dominant phyla in all three seasons. The abundance of Proteobacteria was the highest, with a seasonal difference of spring > autumn > summer. The Shannon diversity index, Simpson diversity index and Chao1 diversity index of bacterioplankton communities in spring were the lowest, and the difference was significant compared with those. (2) There were significant differences among the bacterioplankton communities in the three seasons. β diversity and component decomposition showed that the differences in the three seasons were mainly driven by species turnover. There was a significant trend of geographic distance attenuation in each season, and the decline rate was the fastest in autumn. (3) The Neutral Community Model and the Modified Stochasticity Ratio showed that the stochastic process dominated the assembly of the bacterioplankton communities in spring, while the deterministic process dominated in summer and autumn. (4) The co-occurrence network analysis showed that the species interactions between bacterioplankton communities in the three seasons was dominated by synergistic effect, and each network exhibited a high degree of modularity. (5) Compared to geographical factors, the bacterioplankton communities are more influenced by environmental factors. The key driving factors affecting the bacterioplankton communities in spring are EC, COD, TN, ALT and DO, while in summer they are TUR, EC and pH. In autumn, TUR, ALT, DO, EC and WT are considered. The results show that the bacterioplankton communities in the river of the southeastern Himalayan basin are driven by geographical distance, species interaction and different environmental factors, and there are seasonal differences.