Mangrove provides a unique ecological niche to different microbes which play various roles in nutrient recycling as well as various environmental activities. The highly productive and diverse microbial community living in mangrove ecosystems continuously transforms dead vegetation and recycle nitrogen, phosphorus, sulphur and other nutrients that can later be used by the plants. Mangrove ecosystems are rich in organic matter, and however, in general, they are nutrient-deficient ecosystems, especially of nitrogen and phosphorus. The present study investigated depth wise variation of Nitrifying bacteria, Nitrogen fixing bacteria, total bacterial population along with nitrate-nitrogen, nitrite-nitrogen and other physicochemical parameters of soil during pre-monsoon, monsoon and post-monsoon periods at three different sampling stations of mangrove sediments viz. deep forest region, rooted region and unrooted region. The microbial population was also found maximum in the deep forest sediment relative to the other two sites. Populations of cultureable microbes were found maximum in surface soil and decreased with increase in depth in Sundarban mangrove environment. A decreasing trend of total microbial load, nitrifying and nitrogen fixing bacteria with increase in depth were recorded throughout the year. Present study revealed the relationship among depth integrated variations of physicochemical components (viz. soil temperature, pH, salinity, nitrite nitrogen and nitrate nitrogen concentration) and total microbial load, nitrifying and nitrogen fixing bacteria microbial populations.