Abstract: The concentrations of total phosphorus (TP) and nitrogen (TN) in different salinity samples in Pearl River estuary were determined by using national seawater analytical method and surface water analytical method, respectively.The accuracy and precision of the two methods were investigated, and the concentrations of TN and TP in different salinity were compared by using the two methods.The experimental results indicated that the two methods showed no significant difference.But the seawater analytical method by using flow injection (FI) showed lower detection limit, more environment friendly and higher efficiency than that of the surface water analytical method.