Cyanobacterial harmful algal blooms are prevalent around the world, influencing aquatic organisms and altering the physico-chemical properties in freshwater systems. However, the response of bacterial communities to toxic cyanobacterial blooms and associated microcystins (MC) remain poorly understood even though global concentrations of MC have increased dramatically in the past few decades. To address this issue, the dynamics of bacterial community composition (BCC) in the water column and how BCC is influenced by both harmful cyanobacterial blooms and environmental factors were investigated on a monthly basis from August 2013 to July 2014 in Lake Taihu, China. Non-metric multidimensional scaling (NMDS) revealed that seasonal variation in BCC was significant, and that the succession of BCC greatly depends on changes in environmental conditions. Redundancy analysis (RDA) results showed that the overall variation of BCC was explained mainly by dissolved oxygen (DO), nitrate nitrogen (NO₃⁻-N), and Microcystis. The alpha biodiversity of the bacterial community was different among months with the highest diversity in February and the lowest diversity in October. Furthermore, significant negative relationships were found between alpha biodiversity indices and Microcystis abundance as well as with intracellular MC concentrations, indicating that Microcystis and associated MC may influence the bacterial community structure by reducing its biodiversity. This study shows that potential associations exist between toxic cyanobacterial blooms and bacterial communities but more investigations are needed to obtain a mechanistic understanding of their complex relationships.