Abstract: The dynamics of size-fractionated phytoplankton along the salinity gradient in the Pearl River Estuary and the adjacent near-shore oceanic water was investigated using microscopic, flow cytometric, and chlorophyll analyses in the early spring (March) and early autumn (September) of 2005. In the inner part of the estuary where salinity was less than 30, the phytoplankton community was dominated by micro- and nano-sized (3–200μm) cells, particularly the diatom Skeletonema costatum, both in early spring and early autumn. In areas where salinity >30, including the mixing zone and nearshore oceanic water, micro- and nano-sized cell populations dominated the phytoplankton assemblage during early spring when influence of river discharge was minimal, whereas pico-sized (≤3μm) cell populations were dominant during early autumn as a result of strong river discharge in the summer, with Synechococcus and pico-eukaryotes being predominant. Picophytoplankton were two orders of magnitude more abundant in early autumn (106 cellsmL−1) than in early spring in the nearshore oceanic water. Nutrients delivered by freshwater input to the estuary were pushed toward high salinity (>30) areas as a result of short residence time, exerting a strong influence on phytoplankton abundance, especially picophytoplankton in the nearshore, otherwise oligotrophic, water. Influenced by high abundance of DIN and limitation in phosphorus, picophytoplankton in the adjacent nearshore oceanic water rose to prominence seasonally. Our results indicate that eutrophication in the Pearl River Estuary not only stimulates the growth of S. costatum in the nutrient-rich areas of the estuary but also appears to promote the growth of Synechococcus and pico-eukaryotes in the adjacent usually oligotrophic oceanic water at least during our autumn cruise. [Copyright &y& Elsevier]