Knowledge on phytoplankton dynamics is important to understand the trophodynamics of aquatic ecosystems. But, the topic remains poorly studied in the context of tropical coastal habitats. The present study describes the community structure and drivers of phytoplankton in different coastal habitats along the northern Bay of Bengal. Data were collected on phytoplankton, zooplankton and a range of environmental variables from the estuarine, mangroves and coral habitats of Bangladesh during dry season from October 2020 to March 2021. Our study found that eco‐hydrological characteristics of the estuarine, mangroves and coral habitats differ from each other, although phytoplankton assemblages in these habitats commonly dominated by diatoms. In the estuary, the main diatom taxa included Coscinodiscus, whereas Ceratium and Chaetoceros were dominant in the coral habitat, and Coscinodiscus and Chaetoceros in the mangroves habitat. The concentration of micronutrients (silicate, nitrate and phosphate) was the most important driver of phytoplankton among all habitats. Zooplankton had a vital role in regulating the phytoplankton community composition in the coral habitat. These results suggest that the phytoplankton dynamics across tropical coastal habitats is largely driven by nutrients, which, when compared, have less influence on the growth of phytoplankton in temperate region.