The influence of hydrodynamics on phytoplankton bloom occurrence/formation has not been adequately reported. Here, we document diurnal observations in the tropical Bay of Bengal’s mid-western shelf region which reveal microphytoplankton cell density maxima in association with neap tide many times more than what could be accounted for by solar insolation and nutrient levels. When in summer, phytoplankton cells were abundant and the cell density of Guinardia delicatula reached critical value by tide caused zonation, aggregation happened to an intense bloom. Mucilaginous exudates from the alga due to heat and silicate stress likely promoted and stable water column and weak winds left undisturbed, the transient bloom. The phytoplankton aggregates have implication as food resource in the benthic region implying higher fishery potential, in carbon dioxide sequestration (carbon burial) and in efforts towards improving remote sensing algorithms for chlorophyll in the coastal region.