The mechanisms of hydrodynamic fluctuation that affect cyanobacterial physiological aspects are still unclear. This study was conducted to screen the effects of hydrodynamic fluctuation on phosphorus (P) uptake by Microcystis aeruginosa. Four levels of circumfluence (0, 100, 200, and 300 rpm) and three concentrations of P (0.5, 2.0, and 5.0 mgL(-1)) were used, and the specific growth rate, cell viability, P uptake kinetic, and alkaline phosphatase activity (APA) were determined. Results showed that M. aeruginosa had a higher specific growth rate, cell viability, and P uptake rate at low and moderate circumfluence, APA increased with a decrease of the cellular P quota (Q(p)). Turbulence at 300 rpm negatively affected the metabolic activity: the P uptake rate and affinity were reduced significantly (p < 0.05), APA decreased due to the high Q(p) (p < 0.05), which led to a decline in the specific growth rate and cell viability. It revealed that hydrodynamics could change P uptake and growth of M. aeruginosa. The P absorption capacity and affinity decreased under high turbulence, which led to the inhibition of cyanobacterial growth. It was deduced that high level of artificial turbulence could be used to decrease the risk of cyanobacterial bloom. On the other hand, increasing additional P loading could enhance the adaptability of M. aeruginosa to turbulence, which weakened the inhibition effect of high turbulence on algal growth, and reduced the effects of artificial turbulence on water bloom.