In a monsoon-affected tropical estuary, oscillations in freshwater discharge during monsoon shifted the phytoplankton blooms from those adapted to low salinity to high salinity and vice versa. Salinity stratification during monsoon (onset and restart after an intermittent break) favored diatom (Skeletonema) bloom in low-saline surface waters. In high-saline, nutrient-rich bottom waters, Fragilariopsis (diatom) bloom was observed during onset of monsoon and persisted till the end of monsoon. The break period in monsoon altered the phytoplankton community leading to mixed species bloom of large-sized diatoms and harmful dinoflagellates (Gymnodinium catenatum and Cochlodinium polykrikoides) under high-saline, nutrient-poor, non-stratified, and transparent water column. Such variations in community should be considered for better understanding the biogeochemistry of monsoon influenced tropical estuaries. The dominance of Skeletonema is determined positively by the extent of low-saline stratified condition whereas most of the observed taxa were favored by high saline, nutrient-poor, and transparent waters