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Seasonal variations in the composition and abundance of phytoplankton were investigated fortnightly at 3 different regions along the Mandovi estuary from June 2007 to May 2008 in relation to salinity and nutrients. A total of 209 species belonging to 7 divisions were identified during the study period. The highest phytoplankton cell density (5.17 × 104 cells L-1) and biomass (7.68 mg m-3 chlorophyll a) were observed in the upper sections during the nonmonsoon period, while the highest diversity (3.46) was observed in the upper section during the monsoon period. Bacillariophyta was the dominant phytoplankton group at 71% of the total species identified. This group was dominated by Pennales (88) over Centrales (60) at all 3 stations. Contributions of Dinophyta, Chlorophyta, Cyanophyta, Haptophyta, Chromophyta, and Chrysophyta to the total species were 25%, 0.5%, 1%, 0.5%, 1%, and 1%, respectively. Dinophyta did not show significant variations in percentage distribution among the 3 sections and seasons. Twenty-six dominant species of phytoplankton, representing all seasons with cell density of >1000 cells L-1, showed spatial adaptability patterns with respect to salinity. Protoperidinium acbromaticum and Alexandrium ostenfeldii were found to grow only during nonmonsoon periods in upper sections and were reported for first time in the present study. Euryhaline Skeletonema costatum and Thalassiothrix frauenfeldii were present throughout the study period. A total of 36 harmful algal bloom-forming species, with 11 toxin-producing species, have been identified. The presence of Streptotheca thamensis acts as an indicator to evaluate water quality.