Floating and aggregation are critical stages in the formation of Microcystis blooms, which are significantly affected by wind and waves. In order to analyze the distribution of Microcystis colonies under wind-driven current, a vertical wave simulator (different amplitudes and periods) was used. Colony size and distribution pattern of Microcystis were observed under static and dynamic conditions. Results show that there existed three vertical distribution patterns of Microcystis colonies in the simulator sur face-aggregation, vertical evenly distribution, and the transition stage). The intensity of disturbance and velocity of vertical flow were critical influential factors. Large colonies (>500 μm) could overcome disturbance easily and float more quickly. Meanwhile, the smaller ones (100-300 pm) had the tendency to mix evenly in the vertical direction. When the intensity of disturbance was reduced, Microcystis colonies floated more quickly. The faster the average vertical flow velocity was, the more well was the distribution of the Microcystis colonies. This paper analyzed the relationships between wave elements and the vertical distribution pattern of Microcystis colonies, which provides valuable information for bloom-forming investigation. The study is crucial for effective management of lakes.