Colony size and morphology influence the vertical migration capacity of Microcystis and therewith the occurrence of surface accumulations or blooms. To explore the influence of wind-induced turbulence on the colony size and morphology of Microcystis in field conditions, a high-frequency field investigation was conducted in an enclosure in Meiliang Bay, Lake Taihu, China, from 26 August to 7 September 2012. A Pearson's correlation analysis indicated that the in situ growth rate of Microcystis was negatively related to surface cell density and positively related to wind speed. Strong wind speed stimulated Microcystis growth by enhancing light transmission due to the homodispersion of Microcystis in the water column. The Microcystis colony size was negatively correlated with wind speed, suggesting that wind-induced turbulence could break up colonies in shallow lakes. The results indicated that Microcystis colonies could be broken up by a turbulence intensity of 2.33×10-5 m2/s3, which corresponds to an average wind speed of 5.00 m/s in a reservoir with 30-m depth. Different Microcystis morphotypes were present and negative relationships were detected between the proportion of Microcystis ichthyoblabe and the proportion of Microcystis wesenbergii and between the proportion of Microcystis aeruginosa and the proportion of Microcystis wesenbergii out of all Microcystis throughout the water column, but more evidence is need to support the hypothesis that the morphology of Microcystis colonies changes over time. Altogether, the results suggest that declining wind speed, driven by climate change, will promote surface blooms of Microcystis due to the formation of larger colonies.