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Seasonal distribution of phytoplankton community and size structure was assessed in three different tropical ecosystems of the western Bay of Bengal viz. estuary (Mahanadi), lagoon (Chilika), and coastal waters (off Gopalpur) in response to ambient hydrobiology. Salinity regimes differentiated the study regions as contrasting ecosystems irrespective of seasons (pre-monsoon, monsoon, post-monsoon). Taxonomic account revealed a total no of 175, 65, and 101 phytoplankton species in the estuary, lagoon, and coastal waters, respectively. Prevalence of marine, brackish, and fresh water types in the coastal waters, lagoon, and estuary, respectively, characterized the contrasting nature of the study regions in hosting the phytoplankton community. In general, phytoplankton abundance was observed in increasing order of coastal waters > estuary > lagoon during post-monsoon and pre-monsoon, while lagoon > coastal waters > estuary during monsoon. Bacillariophyta dominated the phytoplankton community in the estuary and coastal waters during all the seasons. In contrast, the lagoon exhibited a diverse array of phytoplankton group such as cyanophyta, dinophyta, and bacillariophyta during monsoon, post-monsoon, and pre-monsoon, respectively. Over the seasons, microphytoplankton emerged as the dominant phytoplankton size class in the coastal waters. Diversely, nanophytoplankton contributed to major fraction of chlorophyll-a concentration in the estuary and lagoon. Interestingly, pre-monsoon dinophyta bloom (causative species: Noctiluca scintillans with cell density 9 × 10 4  cells·l -1 ) and monsoon bacillariophyta bloom (causative species: Asterionellopsis glacialis 5.02 × 10 4  cells·l -1 ) resulted decline in species diversity. Multivariate statistical analysis deciphered salinity as a major environmental player in determining the distribution, diversity, and composition of phytoplankton communities in the three contrasting environments. Trophic state indices signified the lagoon and estuary as hypereutrophic during all season. The coastal water was marked as highly eutrophic through trophic state index during monsoon and pre-monsoon.