To determine the response of bacterioplankton community to sediment resuspension we set up two different intensities of the sediment resuspension in experimental microcosms. We employed the terminal restriction fragment length polymorphism (T-RFLP), denaturing gradient gel electrophoresis (DGGE) methods to characterize the bacterial community structure. The result demonstrated that the species richness of the bacterioplankton in the treatment with sediment resuspension was higher than that in the controls without sediment resuspension. The bacterioplankton species richness and community diversity in the treatment with weak sediment resuspension (WR) was higher than that with strong sediment resuspension (SR). The relationship between bacterioplankton and environmental factors were investigated using canonical correspondence analysis (CCA) and redundancy analysis (RDA). The CCA and RDA results showed that there was a high degree of correlation between bacterioplankton community composition with Cladocera and particulate phosphorus (PP). It indicates that the sediment resuspension of shallow lakes has a significant effect on the species richness and diversity of bacterioplankton. We speculate the main reason is the dynamics of zooplankton community structure and the function of nutrient concentration influenced by the sediment resuspension.