Bacterioplankton plays an important role in driving lake material circulation and indicating the quality of the lake water environment, etc. Unveiling the spatial patterns and community assembly mechanisms of bacterioplankton in lakes is crucial for revealing the process of lake matter circulation and the status of the aquatic environment. Shallow lakes are characterised by strong hydrodynamic disturbance, and the formation mechanism of the spatial pattern of bacterioplankton community is still unclear. By selecting Lake Taihu, a typical large shallow lake, as the research area, this study focused on revealing the spatial patterns and community assembly mechanisms of bacterioplankton in Lake Taihu through high-throughput sequencing technology, multivariate statistical analysis and ecological model construction. The results showed that (1) Bacterioplankton community compositions could significantly distinguish between the northwestern lake region (algae-dominated regime) and the southeastern lake region (macrophyte-dominated regime) of Lake Taihu, but could not distinguish the community compositions between each bay of the two regions and between the lake centre and its surrounding bays. (2) Bacterioplankton community structures of the algae-dominated regime, the macrophyte-dominated regime and the lake centre were significantly correlated with chlorophyll-a, transparency and total suspended solids, respectively. Overall, the relative contribution of environmental variables to the spatial pattern of bacterioplankton community in Lake Taihu was greater than that of spatial variables. (3) Although heterogeneous selection in the deterministic process, “undominated” processes in the stochastic process and dispersal limitation were the main processes affecting the formation of the spatial pattern of bacterioplankton in Lake Taihu, the spatial pattern of bacterioplankton was dominated by the stochastic processes. (4) The hydraulic mixing driven by the disordered wind field in Lake Taihu could lead to the stochastic dispersal of bacterioplankton community among the lake zones, which was the main reason that the stochastic processes dominated the formation of the spatial pattern of bacterioplankton. The present study reveals the spatial patterns and community assembly mechanisms of bacterioplankton in Lake Taihu, which will be important for a deeper understanding of aquatic microbial biogeography and aquatic microbial ecology.