Six lakes (rivers) in Nanjing, Jiangsu Province, with different nutrient levels, were investigated for the phytoplankton community and dominant species. They were Qingxi River, Hucheng River, Xuanwu Lake, Yueya Lake, Pipa Lake, Qianhu Lake. At the same time, algae growth potential tests (AGP tests) were conducted to examine the growth and competition characteristics of Microcystis aeruginosa and Scenedesmus obliquus in different water bodies. Field investigation found that water bodies with different nitrogen (N) and phosphorus (P) concentration have different dominant species. According to nutrient level of water bodies, Chlorophyta, Cyanophyta, Bacillariophyta and Cryptophyta appeared in sequence as dominant species. When cultured with a single algae species, M. aeruginosa grew better in water bodies collected from Qingxi River, Hucheng River and Xuanwu Lake; while S. obliquus only showed a large maximal cell density when cultured in water with high nutrient levels collected from Qingxi River and Hucheng River. It indicated that N and P demand of S. obliquus may be higher than that of M. aeruginosa. When cultured with multi-species, S. obliquus dominated in water body of Qingxi River, and M. aeruginosa dominated in water body of Xuanwu Lake. But the algae could not grow in other water bodies. It indicated that cyanobacteria will not be dominant phytoplankton in waters with too high or too low N and P concentrations. N and P enrichment experiments were conducted using water from Xuanwu Lake, Hucheng River, Yueya Lake and Qianhu Lake, whitch had low N and P levels. The concentrations of N and P would influence the growth of algae, while the concentrations increased, the risk of blooms would increase. Through field investigation and AGP text to explore the relationship between the formation of cyanobacteria and the level of nutrient in water, which provided a scientific basis for revealing the cyanobacteria bloom is the product of eutrophication lake to a certain stage. It is difficult to produce cyanobacteria bloom with too low or too high N and P concentrations.