The size-fractionated phytoplankton biomass and primary production were investigated in four contrasting areas of Hong Kong waters in 2006. Phytoplankton biomass and production varied seasonally in response to the influence of the Pearl River discharge. In the dry season, the phytoplankton biomass and production were low (<42 mg chl m-2 and <1.8 g C m-2?day-1) in all four areas, due to low temperatures and dilution and reduced light availability due to strong vertical mixing. In contrast, in the wet season, in the river-impacted western areas, the phytoplankton biomass and production increased greater than five-fold compared to the dry season, especially in summer. In summer, algal biomass was 15-fold higher than in winter, and the mean integrated primary productivity (IPP) was 9 g C m-2?day-1 in southern waters due to strong stratification, high temperatures, light availability, and nutrient input from the Pearl River estuary. However, in the highly flushed western waters, chl a and IPP were lower (<30 mg m-2 and 4 g C m-2?day-1, respectively) due to dilution. The maximal algal biomass and primary production occurred in southern waters with strong stratification and less flushing. Spring blooms (>10 姠chl?a?L-1) rarely occurred despite the high chl-specific photosynthetic rate (mostly >10 姠C 姠chl?a -1?day-1) as the accumulation of algal biomass was restricted by active physical processes (e.g., strong vertical mixing and freshwater dilution). Phytoplankton biomass and production were mostly dominated by the >5-孠size fraction all year except in eastern waters during spring and mostly composed of fast-growing chain-forming diatoms. In the stratified southern waters in summer, the largest algal blooms occurred in part due to high nutrient inputs