The characters of the morphological, vertical and spatial distribution of nitrogen and phosphate in the water of Changjiang Estuary were discussed, according to the survey conducted in November 2003. Among the dissolved inorganic nitrogen species, nitrate accounted for 90% in the water of Changjiang Estuary. The concentration of nitrogen nutrients in the Changjiang Estuary show higher level, and 67% of sampling stations attained or exceeded the forth standard level of seawater, according to the national standard of seawater quality. Most of total phosphate in the water of Changjiang Estuary is total dissolved phosphate (TDP), which primary composition is dissolved organic phosphate (DOP). The dramatic changes of salinity in the water of Changjiang Estuary lead to the different distribution characteristics of nutrients. The concentrations of nitrate are higher inside the estuary and lower outside the estuary due to its conservatism. On the contrast, ammonium and phosphate are influenced by the change of particle concentrations and salinity, which are higher outside the estuary and lower inside the estuary. Besides, the contents of COD in the water of Changjiang estuary are very high, and the spatial distribution characteristics are higher inside the estuary and lower outside the estuary.