Red tides and eutrophication have been frequently observed over the past two decades in coastal waters around Hong Kong, which are caused by many factors and one of them is the nutrient from nonpoint source pollution (NSP). This paper concentrates on the nutrients carried by river flow from watersheds. Since there are no systematical data sets of nonpoint source pollution in Hong Kong, monthly river water quality measurements, rainfall and river flow data, land uses, and other related information are used to analyze the characteristics of NSP and estimate the nutrient loads for Hong Kong region. Main achievements are as follows: firstly, besides mean concentration for single land use, the concept of integrated mean concentration for mixed land uses was proposed and applied. Secondly, mean concentrations were carried out for different land uses (agriculture, town, grassland, shrubland and woodland), each Water Control Zone, and Hong Kong region. Thirdly, the annual nutrient loads were estimated, for the first time in this paper, with various methods for the whole area of Hong Kong, and about 8000 tons of TN and 1500 tons TP are transported into coastal waters from Hong Kong's land in 1998.