Stratified tropical oceanic systems are in general observed with Subsurface Chlorophyll Maxima (SCM), which was identified as light adaptation of shade-loving picophytoplankton groups. Apart from the light adaptation strategies of phytoplankton, the physical properties of water masses have significant role to hold the phytoplankton in particular layers. The present study gives theoretical explanation on the influence of fluid properties of water on the settling velocities of micro-nano phytoplankton groups, which contribute the SCM. The data and samples were collected from North Eastern Arabian Sea (NEAS) during March (Spring Inter Monsoon), by means of Bio-Argo floats, CTD and remote sensing. The analysis gives indications to the possible strengthening of SCM in the scenario of warming and enhanced stratification. The study conducted simulations using basic stoke’s equations on most abundant species of the area and found that the fluid density has a significant role in the settling of non-motile, suspended phytoplankton groups, irrespective of their cellular density. The simulations show strong decelerations at the same depths, in the upper part of the pycnocline but with varying settling velocity. A numerical expression derived based on curve fitting and multiple regression analysis substantiates the influence of vertical density on SCM. The sensitivity analysis (Global sensitivity Analysis) indicates warming trend in NEAS strengthening the stratification, which in turn influences the concentration in SCM and is capable of altering the primary production.