The Bay of Bengal (BoB) is strongly density stratified due to large freshwater input from various rivers and heavy precipitation. This strong vertical stratification, along with physical processes, regulates the transport and vertical exchange of surface and subsurface water, concentrating nutrients and intensifying the oxygen minimum zone (OMZ). Here, we use basinwide measurements to describe the spatial distributions of nutrients, oxygen, and phytoplankton within the BoB during the 2013 northeast monsoon (November–December). By the time riverine water reaches the interior bay, it is depleted in the nutrients nitrate and phosphate, but not silicate. Layering of freshwater in the northern BoB depresses isopycnals, leading to a deepening of the nutricline and oxycline. Oxygen concentrations in the OMZ are lowest in the north (<5 µM). Weak along-isopycnal nutrient gradients reflect along-isopycnal stirring between ventilated surface water and deep nutrient-replenished water. Picoplankton dominate the phytoplankton population in the north, presumably outcompeting larger phytoplankton species due to their low nutrient requirements. Micro- and nanoplankton numbers are enhanced in regions with deeper mixed layers and weaker stratification, where nutrient replenishment from subsurface waters is more feasible. These are also the regions where marine mammals were sighted. Physical processes and the temperature-salinity structure in the BoB directly influence the OMZ and the depth of the oxycline and nutricline, thereby affecting the phytoplankton and marine mammal communities.