To investigate the temporal and spatial distributions of phytoplankton, inorganic and organic nitrogen as well as their relationship, the phytoplankton and surface water samples were collected at nine sites in Rivers Jiehe, Baozhengang, and Bayaogang in Chongming Island in January, April, July and October of 2014, a sample in Chongxi gate site was also collected as control. These results indicated that the phytoplankton community was composed by chlorophyta and bacillariophyta, and the contribution of euglenophyta biomass was more than 50% in the Chongxi gate and River Baozhengang in summer. Dissolved inorganic nitrogen(DIN) constituted the major fraction of total dissolved nitrogen(TDN), and the percentages of dissolved organic nitrogen(DON) in TDN in the Chongxi gate, Rivers Jiehe and Baozhengang were lower in summer and autumn than those in winter and spring, the release from agriculture soil may be an important source of DON. The concentration of ammonium nitrogen was affected by water temperature, dissolved oxygen, and chemical oxygen demand. The redundancy analysis suggested that the distribution of Chlorophyta and Euglenophyta was affected by ammonium nitrogen, and the distribution of Pyrrophyta was affected by urea.