Spatial distribution and temporal dynamics of phytoplankton community and their relationships with environmental factors were studied in the Pearl River Estuary(PRE), South China, in three seasons. Salinity was considered as the key environmental variable controlling horizontal distributions of phytoplankton community composition. A transition from dominance of freshwater diatoms(Aulacoseira granulata and A. granulata v. angustissima) to estuarine species(Skeletonema costatum and Pseudonitzschia delicatissima) was observed in the high flow season(summer) along the estuary gradient; in the low flow season(spring), the inner estuary was relatively homogeneous and some typical estuarine species could be found near the river mouth. In the normal flow season(autumn), a potentially toxic bluegreen species, Microcystis spp. was predominant in the middle reaches of the estuary, which should be seeded from upstream and transported downstream by river discharges. Phytoplankton abundance was negatively correlated with suspended solid content and nutrient concentration in the PRE, suggesting that turbidity and nutrient availability were the crucial factors regulating the algal biomass. Phytoplankton abundance in the outer estuary was enhanced by increasing irradiance and continued to be enhanced until phosphorus-limitation. Spatial distribution and temporal dynamics of phytoplankton community and their relationships with environmental factors were studied in the Pearl River Estuary (PRE), South China, in three seasons. Salinity was considered as the key environmental variable controlling horizontal distributions of phytoplankton community composition. A transition from dominance of freshwater diatoms (Aulacoseira granulata and A. granulata v. angustissima) to estuarine species (Skeletonema costatum and Pseudonitzschia delicatissima) was observed in the high flow season (summer) along the estuary gradient; in the low flow season (spring), the inner estuary was rather homogeneous and some typical estuarine species could be found near the river mouth. In the normal flow season (autumn), a potentially toxic blue green species, was predominant in the middle reaches of the estuary, which should be seeded from upstream and 运 downstream by river discharges. Phytoplankton abundance was nega suggesting that turbidity and nutrient availability were the crucial factors regulating the algal biomass.