Bacterioplankton play an important role in freshwater ecosystems such as rivers. To explore the seasonal dynamics and driving mechanisms of bacterioplankton communities in the Yarlung Zangbo River basin in the southeastern Himalayas, we analyzed the diversity, biogeographical patterns and driving factors of bacterioplankton communities at 33 different sites over the course of a year using 16S rRNA high-throughput sequencing technology. Our focus was on spring (May), summer (July) and autumn (September). The results showed that: (1) Proteobacteria, Actinobacteriota, Bacteroidota and Cyanobacteria were the dominant phyla throughout the year. Proteobacteria had the highest abundance, with spring having the highest abundance, followed by autumn and then summer. The bacterioplankton community diversity indices (Shannon, Simpson and Chao1) in spring were the lowest and differed significantly from those in the other seasons. (2) Significant differences were observed among the bacterioplankton communities in the three seasons, with β diversity and component decomposition indicating that these differences were primarily driven by species turnover. A significant trend of geographic distance attenuation was observed in each season, with autumn experiencing the fastest decline rate. (3) The Neutral Community Model and the Modified Stochasticity Ratio indicated that stochastic processes dominated the assembly of bacterioplankton communities in spring, whereas deterministic processes dominated in summer and autumn. (4) Co-occurrence network analysis revealed that the interactions between species in the bacterioplankton communities during the three seasons were primarily synergistic and that each network exhibited a high degree of modularity. (5) Bacterioplankton communities are influenced more by environmental factors than geographical factors. The key factors affecting bacterioplankton communities in spring are electric conductivity (EC), chemical oxygen demand (COD), total nitrogen (TN), altitude (ALT) and dissolved oxygen (DO), whereas in summer they are turbidity (TUR), electric conductivity (EC) and pH. In autumn, the key factors are altitude (ALT), dissolved oxygen (DO), electric conductivity (EC) and water temperature (WT). These results demonstrate that bacterioplankton communities in the rivers of the southeastern Himalayan basin are influenced by geographical distance, species interactions and various environmental factors, with differences observed across seasons.