To study the inhibiting effect of aquaculture water of Salvinia natans (L.) All. on Microcystis aeruginosa and the mechanism.Microcystis aeruginosa of 7.5 x 10(5) cells/mL was treated by the culture water of Salvinia natans density of 5%, 10%, 20% and 40%, respectively. The inhibition ratios were calculated, conductivity of algal cells, content of nucleic acid and protein in algae solution, influence of superoxide dismutase (SOD) activity and malondialdehyde (MDA) content were measured.The inhibition rate of 40% treatment group up to 100% on the fourth day. The inhibition rate of 5% treatment group up to 65% on the 7th day. The conductivity of algae cell gone up while the concentration of cultured water was increasing, as well as its content of nucleic acid, protein and MDA. However, the activity of SOD rose at first and then fall down while the concentration of cultured water of Salvinia natans was increasing.The aquaculture water of Salvinia natans has a powerful inhibitory effect on Microcystis aeruginosa by changing the structure of algal cells and intracellular enzyme activity, etc.