We assessed the bacterioplankton community structures from two stations in the Sundarbans mangrove ecoregion. One station (Stn1) is located in the Chemaguri creek and the other station (Stn3) is located in the Mooriganga estuary. These two stations are connected by a continuous stretch of water where freshwater flows from Stn1 toward Stn3 and saline water of Bay of Bengal inflows from Stn3 toward Stn1. Continuous freshwater flow along with diurnal tidal intrusion and heavy seasonal precipitation causes wide range salinity variation in this region. It is expected that the study site could harbour members of the bacterioplankton communities that could be freshwater or marine water organisms. At the same time, some resident members could be adapted such as to show typical 'estuarine' characteristics.