A multianalysis method-polar ordination and cluster-was adopted to investigate the structure of phytoplankton of Wuhan lakes.By comparing the results of ordination and water quality classification, It was proved that the structrual characteristics of the phytoplankton of Lake Donghu and Lake Longyang do not conform to their water quality status due to human disturbances.Hence, the ecological explain was accepted in the article and also some scientific ecological measures were endued to manage and protect the Wuhan's water environment.