The membrane integrity of cells is significant for the safe and effective removal of cyanobacterial cells from drinking water sources. In this paper, cell density counting, cell viability testing, chlorophyll-a determination, extracellular MC-LR monitoring and PCR–DGGE analysis were applied to assess the effects of coagulant dose, shear and floc storage time on the integrity of Microcystis ... [Show full abstract] aeruginosa FACHB-905. Results showed that all cells were removed without damage to membrane integrity under the optimum coagulation conditions: coagulant dose 15 mg/L AlCl3, rapid mix speed 250 r/min, rapid mix time 1 min, slow mix speed 20 r/min, slow mix time 20 min. The coagulant dose and shear did not cause the lysis of cells and ensuing release of MC-LR. But when the flocs were stacked over 6 days, the cells lysed and the MC-LR concentration increased above the background level. In addition, the degree of cell breakage without coagulation was higher than the coagulated cells in flocs. Therefore, keeping the flocs safely treated or disposed of on time as well as keeping the cyanobacterial cells integrally removed plays an important part in controlling the harm of blooms to drinking water production.