Phytoplankton abundance, composition and size-fractionated chlorophyll a (micro-, nano- and pico-chl. a) in the Pearl River Estuary (PRE), South China were assessed in three surveys (Aug. 2010, Jan. 2011 and Aug. 2011) to identify key environmental indicators that shape their distribution patterns. Non-metric multidimensional scaling (MDS) showed that the PRE formed three regional clusters that were characterized by a transition from dominant freshwater species to estuarine diatoms in normal summer flow conditions (Aug. 2010). With a reduced river flow in winter (Jan. 2011), the inner estuary was categorized as one group marked by the predominance of the nanoflagellate, Plagioselmis prolonga. This small-sized cryptophyte was first recorded in the PRE and was likely to outcompete other phytoplankton species in turbid or well-mixed waters. During the extreme drought of summer of 2011 (Aug. 2011), the estuarine plume was limited and regional division by MDS was similar to winter patterns, as some marine species were observed in the upper estuary. We considered that the higher phytoplankton density in the summer of 2011 was presumably a combined effect of longer residence time and higher phosphate concentration. With respect to the size-fractionated phytoplankton composition, our results showed that almost half of the chl. a in the estuary was contained in microplankton particles, while the proportion of pico-chl. a increased from the upstream of the PRE towards the estuary boundary (Wanshan Islands). Furthermore, phytoplankton abundance, three size classes of chl. a and environmental factors were explored by principal component regression (PCR) analysis. In three surveys, pico-chl. a was negatively correlated with the first principal component (PCL, positively loaded with salinity and inversely with inorganic nutrients), which indicated a negative influence of the riverine and coastal waters on picophytoplankton and the specific oligotrophic niche of picophytoplankton. Similarly, PC1 was also considered as the key environmental variable basis controlling micro-chl. a in summer of 2010, while in the summer of 2011, zooplankton and copepods were positively associated with phytoplankton abundance, suggesting a resource effect of phytoplankton on zooplankton development.