The tropical estuarine ecosystem is fascinating for studying the dynamics of water quality and phytoplankton diversity due to its frequently changing hydrological conditions. Most importantly, phytoplankton is the main supplier of ω3 polyunsaturated fatty acids (PUFA) in the coastal food web for fish as they could not synthesize PUFA. This study evaluated seasonal variations of water quality parameters in the Meghna River estuary (MRE), explored how phytoplankton diversity changes according to hydro-chemical parameters, and identified the major phytoplankton groups as the main source of PUFA for hilsa fish. Ten water quality indicators including temperature, dissolved oxygen, pH, salinity, dissolved inorganic nitrogen (DIN=nitrate, nitrite, ammonia) and phosphorus, dissolved silica and chlorophyll-a were evaluated. In addition, phytoplankton diversity was assessed in the water and hilsa fish gut. Principal component analysis (PCA) was used to analyze the spatio-temporal changes in the water quality conditions, and the driving factors in the MRE. Four main components were extracted and explained 75.4% variability of water quality parameters. The most relevant driving factors were dissolved oxygen, salinity, temperature, and DIN (nitrate, nitrite and ammonia). These variabilities in physicochemical parameters and dissolved inorganic nutrients caused seasonal variations in two major groups of phytoplankton. Peak abundance of chlorophyta (green algae) occurred in water in nutrient-rich environments (nitrogen and phosphorus) during the wet (36 %) season, while bacillariophyta (diatoms) were dominant during the dry (32%) season that depleted dissolved silica. Thus, the decrease of green algae and increase of diatoms in the dry season indicated the potential link to seasonal changes of hydro-chemical parameters. The green algae (53.7 %) were the dominant phytoplankton group in the hilsa gut content followed by diatoms (22.6 %) and both are contributing as the major source of PUFAs for hilsa fish according to electivity index as they contain the highest amounts of PUFAs (60 and 28% respectively).