A comprehensive survey is undertaken in the upper reaches of the Taihu Lake watershed,including Gehu Lake,Taige Canal and the Caoqiao River. Results of the analysis of water samples from 12 sampling sites show all of these waters are high in nutrient content,being hyper-eutrophicated. It is found through PCA integrated assessment that water quality in most of the rivers'sections is on the level of Class IV,the Lake level of Class III. Aquatic ecological investigation in terms of aquatic plants indicate that diversity of aquatic plants are very low,represented by water hyacinth and common duckweed,the dominant species widespread over the rivers and canal;the submersed macrophytes,as a whole,have showed serious tendency of decline,and their distribution areas are on decrease. Cluster analysis method of UPGMA is used to categorize the aquatic macrophytes which have been investigated,and through PCO and CCA analysis,there was a distinct separation between rivers and lake in terms of physio-chemical factors of the waters. It is concluded that the aquatic environmental factors such as N and P in their various forms,both in water and in the sediment,have exerted influences on the plants in terms of composition and distribution.