Water and sediment are two different but closely related habitats in the lake ecosystem, and the bacteria inhabiting these two habitats play a key role in maintaining the ecosystem balance and driving elemental cycling. To investigate the distribution patterns of bacterial communities in lake water and sediment, this paper investigated the bacterial communities in water and sediment in four regions of Lake Taihu, and analysed the bacterial community composition and diversity levels, distribution characteristics and their drivers in these two types of habitats based on high-throughput sequencing technology and statistical analysis. The results showed that Actinobacteria, Proteobacteria and Cyanobacteria were the main bacteria in the surface water bacterial community, while Proteobacteria dominated in the surface sediment. In the two habitats, bacterial richness and local contribution to beta diversity (LCBD) were relatively higher in the western region of Lake Taihu, and the community structure showed significant regional differences. For surface water bacterial communities, the important factors influencing community richness were water conductivity, pH, sediment porosity and PC1 (principal component of heavy metal elements), while the important factors influencing community uniqueness were PC1, water temperature and pH. In addition, network complexity increased significantly with increasing pH. For surface sediment bacterial communities, total phosphorus and lithium were the most important factors influencing community richness and community uniqueness. Furthermore, network complexity decreased with increasing metallic element content, whereas it increased with increasing total phosphorus, ammonium and phosphate concentrations in the sediment. These results showed that the bacterial communities in the water and sediment were driven by different environmental factors, providing a new perspective for aquatic ecosystem conservation and water resource management in Lake Taihu.