A regional Earth System Model has been implemented for the South Asia region. We investigate the effect of the marine biogeochemical feedback which affects the attenuation of the short-wave radiation upon the regional climate. In the experiment where the feedback is activated the average SST is lower over most of the domain. The greatest deviations (more than 1°C) in SST between the two runs occur in the summer period during the phytoplankton bloom. A significant cooling of subsurface layers occurs and the thermocline shifts upward compared to the Jerlov type absorption. The phytoplankton primary production and its deviation in the feedback-based simulation turned out to be higher, especially during periods of winter and summer phytoplankton blooms. The marine biogeochemistry feedback also affects the amount of precipitation in the model in particular during the monsoon season. The associated SST cooling leads to a reduction of the precipitation but affects it in different ways. In the Arabian Sea, the reduction of the transport of humidity across the equator leads to a reduction of the large scale precipitation in the eastern part of the basin, reinforcing reduction of the convective precipitation. In the Bay of Bengal, the feedback increases the large scale precipitation, contouring the decrease of convective precipitation. Thus, the main impacts of including the biogeochemical coupling in the Indian Ocean include the enhanced phytoplankton primary production, a shallower thermocline and decreased SST, with cascading effects upon the model ocean physics which further translates into altered atmosphere dynamics.