Abstract: The migration and distribution of Microcystis colonies under waves are of great significance for understanding Microcystis blooms. This work experimentally investigates the trajectory, concentration distribution, and aggregation of Microcystis colonies in small amplitude waves. Results show that, unlike the approximately vertical upward migration trajectory in still water, the Microcystis colonies show periodic motion in waves but still show an upward trend. The closer the Microcystis colonies are to the water surface, the greater the influence of water waves on them. The larger the wave height, the stronger the water carrying capacity caused by water waves, the more extensive the periodic movement range of the Microcystis colonies, and the more uniform in the vertical direction. For the large wave height, the Microcystis colonies floating on the surface are prone to fragmentation and dispersion by water waves into the lower water layer. Large-scale Microcystis populations have strong vertical autonomous migration ability and tend to aggregate on the water surface, forming higher surface concentrations. However, small-scale Microcystis colonies have weak autonomous migration and are easily carried by water waves to the lower layer of water, with relatively uniform vertical distribution.