Western tropical Indian Ocean, Arabian Sea, and the equatorial Pacific are known as regions of intense bio-chemical-physical interactions: the Arabian Sea has the largest phytoplankton bloom with seasonal signal, while the equatorial Pacific bloom is perennial with quasi-permanent upwelling. Here, we studied three dimensional ocean thermodynamics comparing recent ocean observation with ocean general circulation model (OPYC) experiment combined with remotely sensed chlorophyll pigment concentrations from the Coastal Zone Color Scanner (CZCS). Using solar radiation parameterization representing observations that a higher abundance of chlorophyll increases absorption of solar irradiance and heating rate in the upper ocean, we showed that the mixed layer thickness decreases more than they would be under clear water conditions. These changes in the model mixed layer were consistent with Joint Global Ocean Flux Study (JGOFS) observations during the 1994-1995 Arabian Sea experiment and epi-fluorescence microscopy (EFM) on samples collected during Equatorial Pacific Ocean Climate Study (EPOCS) in November, 1988. In the Arabian Sea, as the chlorophyll concentrations peak in October (3 mg/m³) after the summer plankton bloom induced by coastal upwelling, the chlorophyll induced biological heating enhanced the sea surface temperature (SST) by as much as 0.6‡C and sub-layer temperature decreases and sub-layer thickness increases. In the equatorial Pacific, modest concentrations of chlorophyll less than 0.3 mg/m³ is enough to introduce a meridional differential heating, which results in reducing the equatorial mixed layer thickness to more than 20 m. The anomalous meridional tilting of the mixed layer bottom enhances off equatorial westward geostrophic currents. Consequently, the equatorial undercurrent transports more water from west to east. We proposed that these numerical model experiments with use of satellite andin situ ocean observations are consistent under three dimensional ocean circulation theory combined with solar radiation transfer process.