Abstract: Study on cyanobacteria outbreak caused by lack eutrophication, which is a global environment problem, has practical significance. Eutrophication process plays a key role in cyanobacteria outbreak, and caused water quality deterioration. In experimental under natural water environment from 12th,Aug, 2012 to 3rd,Sep,2012, through analysis on the differences of TN, TP and Chl a between enclosures with cyanobacteria and open water with no cyanobacteria, we studied the effects of Cyanobacteria accumulation on water environment and growth of submerged macrophytes. Results showed that: in enclosure with accumulation of cyanobacteria, the TN, TP and Chl a were higher than in open water contrast. Cyanobacteria accumulation resulted declining in biomass of the whole submerged community, and compares to great increase in open water contrast. Then comes to the conclusion: cyanobacteria accumulation caused nutrients increase in water environment, and then leaded to the density increase of alage and decrease of most submerged macrophytes except Myriophyllum verticillatum.