Lake Caohai has experienced extensive Microcystis blooms in recent years, and to improve its water quality, the local government carried out a series of water control measures. To better understand the dynamics of both pelagic and benthic Microcystis and their characteristics in Lake Caohai, we conducted a 1-year investigation from December 2015 to December 2016 to gain a seasonal outlook on the distribution and dynamics of cell abundance, colony size and intracellular microcystins (MCs) of Microcystis. The results indicated that the Microcystis bloom occupied primarily the northeastern region and then moved gradually from lakeshore to lake center. The perennial southwesterly winds and the water inflow from northeast to southwest in Lake Caohai determined the spatiotemporal distribution of pelagic Microcystis. Benthic Microcystis was mainly distributed in the northeastern region in summer, occupied the lake center in autumn and then occupied the southeastern region in winter, determined by the sedimentation of pelagic Microcystis and the death of benthic Microcystis. Small colonies (20-60 mu m) overwintered more easily in both water column and sediment. The concentrations of intracellular toxin of benthic Microcystis were observed to be significantly higher than those of pelagic Microcystis. This might be because Microcystis synthesized large amount of MCs to acclimate to an unfavorable benthic environment. This knowledge on the dynamics of Microcystis expands our understanding of mechanisms underpinning the formation of Microcystis blooms. (c) 2019 The Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V.