This study investigated the seasonal and spatial dynamics of nutrients and phytoplankton biomass at 12 stations in Hong Kong (HK) waters during a three year period from 2004 to 2006 after upgraded sewage treatment and compared these results to observations before sewage treatment. Pearl River estuary (PRE) discharge significantly increased NO(3) and SiO(4) concentrations, particularly in western and southern waters when rainfall and river discharge was maximal in summer. Continuous year round discharge of sewage effluent resulted in high NH(4) and PO(4) in Victoria Harbour (VH) and its vicinity. In winter, spring and fall, the water column at all stations was moderately mixed by winds and tidal currents, and phytoplankton biomass was relatively low compared to summer. In summer, the mean surface phytoplankton chl biomass was generally > 9 microL(-1) in most areas as a result of thermohaline stratification, and high nutrients, light, and water temperature. In summer, the potential limiting nutrient is PO(4) in the most productive southern waters and it seldom decreased to limiting levels ( approximately 0.1 microM), suggesting that phytoplankton growth may be only episodically limiting. The mean bottom dissolved oxygen (DO) remained > 3.5 mg L(-1) at most stations, indicating that the eutrophication impact in HK waters was not as severe as expected for such a eutrophic area. After the implementation of chemically enhanced primary sewage treatment in 2001, water quality in VH improved as indicated by a significant decrease in NH(4) and PO(4) and an increase in bottom DO. In contrast, there were an increase in chl a and NO(3), and a significant decrease in bottom DO in southern waters in summer, suggesting that hypoxic events are most likely to occur in this region if phytoplankton biomass and oxygen consumption keep increasing and exceed the buffering capacity of HK waters maintained by monsoon winds, tidal mixing and zooplankton grazing. Therefore, future studies on the long-term changes in nutrient loading from PRE and HK sewage discharge will be crucial for developing future strategies of sewage management in HK waters.