To explore the variation of phytoplankton community along the Bakkhali river estuary and its adjacent coastal water in the north of the Bay of Bengal, total Chl-a (TChl-a) concentrations and group-specific photosynthetic pigments were investigated during April 2017. Distinct spatial distribution was observed in temperature, turbidity and nutrient concentrations as well as in TChl-a concentrations, showing a seaward decreasing pattern. The different distribution of phytoplankton pigments and functional groups along the gradients was also observed. Chlorophyll-b and zeaxanthin showed their highest abundance in the turbid riverine water, while alloxanthin and prasinoxanthin dominated in the coastal water. High concentrations of fucoxanthin, peridinin and hex-fucoxanthin were associated with high-light availability and showed a seaward increasing trend. Three phytoplankton groups can be classified: the riverine group (chlorophytes and cyanobacteria), the coastal group (cryptophytes and prasinophytes) and the offshore group (diatoms, dinoflagellate and haptophytes_type 6). The predominance of cryptophytes (avg. 48%) over diatoms (avg. 28%) was basically influenced by the scarcity of nitrogen and silicate relative to phosphate. Not only availability of nutrients, the photosynthetically active radiation also plays a key role in regulating TChl-a, photosynthetic pigments and functional groups in this tropical estuarine-coastal zone.