Data on ocean color chlorophylla (Chl a) obtained using Sea-viewing Wide Field of view Sensor (SeaWiFS), sea surface temperature (SST) by Advanced Very High Resolution Radiometer (AVHRR), and sea surface height (SSH) by TOPEX/POSEIDON were analyzed to examine the influence of Indian Ocean Dipole (IOD) on the physical and biogeochemical processes with special reference to phytoplankton primary production and air-sea fluxes of carbon dioxide in the Arabian Sea. Positive SST anomalies (SSTA) were found in the Arabian Sea (0.4 to 1.8°C) with higher values in the southwestern Arabian Sea that decreased towards north. The SSH anomalies (SSHA) and turbulent kinetic energy anomalies (TKEA) suggest decreased mixing during the IOD compared to the normal period. Chlorophylla displayed significant negative correlations with SSTA and SSHA in the Arabian Sea. Consistently, Chla showed negative anomalies (low Chl a) during the IOD period which could be due to reduced inputs of nutrients. The photic zone integrated primary production decreased by 30% during the IOD period compared to the normal whereas pCO2 levels were higher (by 10–20μatm). However, sea to air fluxes were lower by 10% during the IOD period due to prevailing weaker winds. Primary production seems to be the key process controlling the surface pCO2 levels in the Arabian Sea. In future, the influence of IOD on ecosystem structure, export production and bacterial respiration rates are to be probed throughin situ time-series observations.