Cyanobacterial biomass in water column and sediment were investigated from October 2018 to October 2019 in the center of western Lake Chaohu. Phytoplankton were mainly composed of Microcystis, Crucigenia, Phormidioideae, Cryptomonas and Anabaena. The dominate cyanobacterial genus were Microcystis between May and November, Anabaena between November and December, and Phormidioideae between January and April. Cyanobacterial biomass in water column peaked in September and January, and settled down afterwards, resulting in the two peaks of cyanobacterial biomass in sediment. In comparison with that in water column, cyanobacteria biomass was relatively low in sediment. The proportion of cyanobacterial biomass per unit surface between water column and sediment was more than 100 in June and was relatively low from November to March, with the lowest level being less than 2. Benthic cyanobacteria were mainly distributed on the surface sediment (0-2 cm). The monthly vertical flux of cyanobacterial biomass was monitored by using an in situ trap. Our results showed that cyanobacterial biomass settled massively from water column to sediment in November and February. Cyanobacteria tended to have upward migration from sediment to water column in November and June, caused by large cyanobacterial biomass in sediment and high turbulence. However, the active recruitment of benthic cyanobacteria was low throughout the whole year. The best period to reduce the cyanobacterial seed from sediment is from October to February. However, this might not function well to mitigate cyanobacterial bloom in summer, since cyanobacteria biomass is lower in sediment than in water column and the contribution of recruitment is small.