© 2015 by the authors; licensee MDPI, Basel, Switzerland. Flavonoids are natural polyphenolic compounds produced by many aquatic plants and released in their environments. In this study, the effects of several aquatic flavonoids on cyanobacterial Microcystis aeruginosa, especially in relation to the cell growth, photosynthetic activity, cell morphology, and cell membrane integrity, were investigated. Significant growth inhibition was observed when the cyanobacteria were exposed to three flavonoids, namely, 5,4'-dihydroxyflavone (DHF), apigenin, and luteolin. Luteolin reduced the effective quantum yield, photosynthetic efficiency, and maximal electron transport rate by 70%, 59% and 44%, respectively, whereas 5,4'-DHF and apigenin slightly affected these parameters, which implies that luteolin disrupts the photosynthetic system. Moreover, 5,4'-DHF and apigenin compromised the membrane integrity, and induced membrane depolarization in 52% and 38%, and permeabilization in 30% and 44% of the cells, respectively. The 5,4'-DHF and apigenin showed more pronounced effects on M. aeruginosa morphology and membrane integrity, compared to the luteolin. These results suggest that flavonoids could have significant effects on growth and physiological functions in cyanobacterial species.