In this paper, a mathematical model coupling buoyancy regulation model and hydrodynamic model was developed to simulate the trajectory of Microcystis colonies in calm water. The simulation results showed that Microcystis present different movement trajectories in water with different depths. In shallow water where large amounts of incident light could reach at the bottom of water, all the Microcystis colonies, whatever size they have, stayed at the bottom. However, in deep water, again whatever size they have, Microcystis colonies made periodical movements. The simulation results revealed that colony size was the main factor that determined the trajectory amplitude in the vertical. The Microcystis colony with larger size would reach deeper positions and also reach water surface. Extinction coefficients determined the movement position. If the extinction coefficient was small, Microcystis colonies would move in the deeper position. On the contrary, if the extinction coefficient was large, the colonies would move near the water surface.