The high-frequency times-series data collected during 28th October to 21st November 2006 onboard R/V Mirai provided the first evidence of short-term bio-physical coupling in the central equatorial Indian Ocean (EIO). The predominant feature of the thermal structure was the down-sloping of 28 degrees C-isotherm and up-sloping of 14 degrees C-isotherm indicating deepening of surface-layer and shoaling of lower-thermocline respectively. Concomitant with the deepening of surface-layer, nitracline and subsurface chlorophyll maximum (SCM) also deepened. From the prominent bi-weekly periodicity in the 14 degrees C-isotherm and the upward phase propagation in the meridional current velocity, we infer that shoaling was the response of mixed Rossby-Gravity (MRG) waves. Based on temperature and currents we propose that deepening of surface-layer was caused by the eastward advection of warmer waters associated with the weakening of Indian Ocean Dipole (IOD). This made the upper ocean more nutrient-depleted and biologically less-productive, an indication that the central EIO is returning to its pre-IOD condition.