Monitoring the primary producer diversity is crucial in understanding ecosystems balance, as imbalanced nutrients richness and diversity may induce red tide situations. The present study deals with evaluating the impact of hydrological factors regulating the dynamics of phytoplankton communities and the influence of chemical parameters on phytoplankton growth in Pearl River Estuary (PRE). During wet season (April), around 50 different species of phytoplankton were identified at 14 different sampling sites including 24 diatoms, 9 dinoflagellates, 10 green algae and 6 cyanobacterial species respectively. The diatom Melosira granulate was the dominant species at most of the sampling sites. Phytoplankton surveys during the dry season (November) showed Bellerochea malleus and Skeletonema costatum species as dominant at most of the sampling locations. Silicate (SiO₃) distribution was one of the reason for the abundance of diatoms in west shoal sites. The concentration of nutrients and hydrological factors like water depth and salinity strongly supported phytoplankton growth. In addition, PRE west and middle shoal sites showed evidence of rich phytoplankton diversity when compared to east shoal and channel sites. The Non-metric Multidimensional Scaling (NMDS) analysis and cluster grouping analysis demonstrated the uniqueness of plankton species diversity at PRE west and east shoal sites. The results of Canonical Correspondence Analysis (CCA) suggested that diversity of phytoplankton communities was significantly influenced by environmental factors such as salinity, depth and SiO₃ concentration. From these results, one may conclude that salinity with SiO₃ distribution plays a crucial role in PRE phytoplankton community composition assisting in maintaining healthy intertidal ecosystem.