In-situ light-availability control is commonly used to suppress Microcystis blooms in nutrient-rich water resources. It has been suggested that the reduction of column cyanobacterial biomass could mostly be attributed to the inhibition of photosynthesis. However, sinking loss may be another factor influencing the column cyanobacterial biomass. To further investigate the mechanism of this reduction, a mixing-static water column experimental apparatus was designed to simulate the reduction of Microcystis biomass under light-availability control. Under light-shading plus mixing, the reduction of Microcystis in the water column was attributed to both intrinsic biomass loss and sinking loss. Comparatively, under light-shading without mixing, the Microcystis accumulated in surface water, maintaining a continuously increase of intrinsic biomass. Meanwhile, the sinking loss increased as the water column became static, even exceeding the increase of intrinsic biomass, suggesting that sinking loss was the main mechanism for the reduction under light-shading. Further investigation indicated that both intrinsic growth rate and sinking loss rate varied in response to available light. Accordingly, a hypothesis is represented that the loss of column biomass and the shift in dominant species under light-availability control are primarily attributed to the combined effects of intrinsic biomass change and sinking loss, which both respond to available light.