In recent years, harmful cyanobacterial blooms frequently occurred all over the world, causing great damage to ecosystems, fishery resources, and recreational facilities. Therefore, the removal of harmful cyanobacterial blooms is a crucial step for the maintenance of safe water supplies and for the safety of aquatic products. Hydrogel beads based on sodium alginate and an aqueous extract from pomegranate peel were prepared, and used for removing Microcystin aeruginosa. The removal efficiencies of hydrogel beads to M. aeruginosa and the factors affecting its removal from solutions (the ratio of material to solvent, the dosage of hydrogel beads, and the density of M. aeruginosa cells) were investigated. The optimum ratio of material to solvent, the dosage of hydrogel beads and the density of M. aeruginosa cells were 0.03 g/cm 3 , 100 g/dm 3 and less than 8.6810 6 cells/cm 3 , respectively. When the density of M. aeruginosa cells was below 8.6810 6 cells/cm 3 , the removal efficiency of cyanobacteria was above 99.21% at the dose of 100 g/dm 3 . The pomegranate peel and sodium alginate, as natural materials, were safe and innocuous, providing simple operation, low cost and high availability. Therefore, the hydrogel beads offer favorable characteristics in M. aeruginosa removal.