AbstractCyanobacterial blooms are one of the most severe ecological problems affecting lakes. The vertical migration of cyanobacteria in the water column increases the uncertainty in the formation and disappearance of blooms, which may be closely associated with light, temperature, and wind speed. However, it is difficult to quantitatively evaluate the influencing factors of cyanobacteria vertical movement in natural environment compared to the laboratory experimental environment. Besides, both field survey and laboratory experiment method have the difficulties in determining the diurnal vertical migration of cyanobacteria at the synoptic lake scale. In this study, based on the diurnal dynamics of cyanobacterial bloom intensity (CBI) observed by the Geostationary Ocean Color Imager (GOCI) from 2011 to 2019, the daily variations, floating rate, and sinking rate of Microcystis aeruginosa were calculated in the natural environment. Then, the effects of light, temperature, and wind speed on the vertical migration of M. aeruginosa were analysed from the perspectives of day, night, and season. The results are as follows: the records of three typical patterns of diurnal CBI exhibited strong seasonal variability from the 9-year statistics; at night, the buoyancy recovery rate of cyanobacterial colonies increased with temperature, so that at temperature >15 °C and wind speed <3 m s−1, CBI reached the maximum of the whole day at 08:16; the sinking rate of M. aeruginosa was positively correlated with the cumulated light energy at both synoptic and pixel scale; the upward migration speed of M. aeruginosa was positively correlated with the maximum wind speed of the day before cyanobacterial bloom. Therefore, the severer cyanobacterial blooms were often observed by satellite images after strong winds. The analysis of diurnal variation, floating rate, and sinking rate of M. aeruginosa will expand our knowledge for further understanding the formation mechanism of cyanobacterial blooms and for improving the accuracy of model simulation to predict the hourly changes in cyanobacterial blooms in Lake Taihu.