The Pearl River Estuary（PRE）, a significant confluence of fresh and saltwater systems in Southern China, plays a crucial role in regional biogeochemical cycles. Phytoplankton serve as vital contributors to global ecosystems as primary producers, sustaining the foundation of the marine food web, facilitating nutrient cycling, and significantly influencing carbon dynamics and climate regulation through photosynthesis. The present study aims to elucidate patterns of distribution, abundance, and species diversity, as well as to identify the key environmental factors driving these dynamics based on the data of 2020. The distribution of phytoplankton species exhibits a decreasing trend in a gradient extending seaward from the estuary.Our findings reveal that diatoms are the dominant group, contributing significantly to the overall chlorophyll a concentrations during summer. Influenced by the freshwater runoff from the Pearl River, there is an abundant variety of phytoplankton in this area, including a significant presence of low-salinity species. The predominant phytoplankton species are dominated by cyanobacteria, specifically including Chroococcus spp., Microcystis spp., Oscillatoria spp., Pseudoanabaena spp., Roperiatesselata sp., and the diatom Melosira granulata. The abundance of phytoplankton exhibits a decreasing trend from upstream to downstream. However, near the Jiaomen Waterway, the abundance of phytoplankton is relatively low due to an inverse thermal phenomenon. The Shannon-Wiener diversity index ranges from 1.289 to 2.932, with an average of 2.050.The Pielou's evenness index ranges from 0.278 to 0.571, with an average of 0.436. The diversity and evenness index are both higher near the Jiaomen Waterway and lower in the Hongqili Latao, indicating a moderate to low level of biodiversity overall. Si and salinity are significantly correlated with the abundant of phytoplankton ((Mantel test; Si: r = 0.2362, P =0.0172; salinity: r = 0.2392, P =0.0254).Our assessment serves as a baseline for monitoring changes in response to anthropogenic pressures such as pollution and climate change.

phytoplankton,the Pearl River Estuary,species characteristics