Studies on damages in photosynthetic activities of Microcystis colonies and effect on their sinking process induced by ultrasound merited are of important practical value, which could provide powerful support for the promotion of ultrasound application in dealing with cyanobaterial blooms. Therefore, these processes have been assessed according to changes of chlorophyll-a (Chl.a) fluorescence and the vertical distribution of the Chl.a content in water column, respectively. Results showed that appropriate ultrasound parameters (35 kHz, 0.0353 W/cm³) did not disrupted algal cells, but significantly inhibited their photosynthetic activities. For example, the photosynthetic activities of Microcystis colonies treated for 60 s had been inhibited by 45.5%. However, the inhibited photosynthetic activities of all treated algae were recovered approximately to 80% of the control within 24 h of culture after treatment. The maximal removal rate of Chl.a from raw water (79.5%) was obtained at 5 s of sonication when cultivation time was up to 0.5 h. More than 90% of algal cells that had been treated for 30 s and then sank to the bottom, resuspended or refloated after 72 h of the culture. However, algal cells treated for 60 s did not refloat during the experiment period (96 h). Changes of colony size played a key role in the sedimentation character during ultrasonication and the recovery process of buoyancy after exposure. Furthermore, when Microcystis colonies were exposed to ultrasound, gas vesicles and photosynthesis pigment were damaged firstly, which followed by the declumping of cyanobacteria markedly.