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Abstract Spatio-temporal variation in phytoplankton community dynamics in a temporarily open/closed Swarnamukhi river estuary (SRE), located on the South East coast of India was investigated and correlated to that of the adjacent coastal waters. Understanding the seasonal variability of the phytoplankton community and influencing factors are essential to predicting their impact on fisheries as the river and coastal region serve as the main source of income for the local fishing communities. Downstream before the river meets the sea, an arm of the Buckingham Canal (BC), carrying anthropogenic inputs empties into the Swarnamukhi River (SR1). The impact of anthropogenic effects on the phytoplankton community at BC was compared to other estuarine stations SR2 (upstream), SR1 (downstream), SRM (river mouth) and coastal station (CS). In BC station, harmful algal blooms (HABs) of Chaetoceros decipiens (2940 × 103 cells L−1) and Oscillatoria sp. (1619 × 103 cells L−1) were found during the southwest monsoon and winter monsoon, respectively. These HABs can be linked to the anthropogenic input of increased nutrients and trace metals. The HABs of Oscillatoria sp. were shown to be induced by elevated concentrations of nitrate (10.18 µM) and Ni (3.0 ppm) compared to ambient, while the HABs of C. decipiens were caused by elevated concentrations of silicate (50.35 µM), nitrite (2.1 µM), and phosphate (4.37 µM). Elevated nutrients and metal concentration from the aquaculture farms, and other anthropogenic inputs could be one of the prime reasons for the recorded bloom events at BC station. During this period, observed bloom species density was found low at other estuarine stations and absent at CS. The formation of bloom events during the closure of the river mouth could be a major threat to the coastal ecosystem when it opens. During the Osillatoria sp. bloom, both the Cu and Ni levels were higher at BC. The elevated concentration of nutrients and metals could potentially affect the coastal ecosystem and in turn fisheries sector in the tropical coastal ecosystem.