Aimed to explore the relationship between Microcystis cells sinking and water bloom development, the physiological status of the sinking cells was characterized by comparing with the floating cells. The sinking ratio and the 3-[4, 5-dimethylthiazol-2-yl]-2, 5-diphenyl tetrazolium bromide (MTT) staining were also employed in surface and bottom samples to substantiate the character. The dynamics of the sinking ratio and the chlorophyll a concentration were also compared. The field Microcystis cells had relative stable positions in the sample container after 2 hours settlement in the lab. Statistic analysis suggested that the floating and the sinking colonies did not differ significantly on the indicators maximum quantum yield of PS II and membrane integrity (p > 0. 05), but did significantly on the electron transfer rate and nicotinamide adenine dinucleotide (phosphate), reduced disodium salt [ NAD (P) H] dependent oxidoreductase and dehydrogenase activities (p < 0.01). Furthermore, comparison between bottom samples and surface samples suggested the bottom had higher ratio of sinking and MTT negative cells (p < 0.01). These results implied that the sinking cells were injured and had lower metabolic activity. During the time from October 2007 to May 2008, the sinking ratio reached climax about 40% in winter, and a negative correlation between the sinking ratio and chlorophyll a concentration was observed (p < 0.05). Sinking played an important role in the decline of Microcystis bloom. A research on the sinking ratio will be helpful for the understanding of bloom development tendency. The characterization on the physiology status of sinking cells constructed basement for the introduction of sinking ratio to the prediction of water bloom development.