The evolution of intermediate circulation in the northern Indian Ocean since the last deglaciation has been reconstructed from two marine cores located at intermediate depths off the southern tip of India (MD77‐191) and in the northern Bay of Bengal (BoB) (MD77‐176). Benthic foraminiferal δ13C, seawater carbonate ion concentration ([CO32‐]) estimated from the Sr/Ca, and paleo‐temperature reconstructed on the basis of the Mg/Li of aragonite benthic species Hoeglundina elegans were used to trace the evolution of past intermediate‐deep water masses and to constrain ocean‐atmosphere exchanges during the two‐stage increase in atmospheric CO2 across the last deglaciation. The intermediate water [CO32‐] was mainly affected by changes in the ocean alkalinity inventory, associated with the modulation of atmospheric CO2 on glacial‐interglacial time scales. Higher benthic foraminiferal δ13C, depleted [CO32‐] and decreased Benthic‐Planktonic 14C age offsets at intermediate water depths suggest a release of deep‐sea CO2 to the atmosphere through the Antarctic Intermediate Water (AAIW) in the Southern Ocean during the 17‐15.2 and 12.6‐10.5 cal kyr BP time intervals. In addition, the decreased H. elegans Mg/Li record seems to reflect an increased contribution of cold water mass during the 17‐15.2, 12.6‐11.9 cal kyr BP intervals and throughout the Holocene. In contrast, two warm events occurred in the 15‐13.3 and 11‐10.3 cal kyr BP time intervals. During the late Holocene, a decrease in the intermediate‐water [CO32‐] indicates a contribution to atmospheric CO2 rise since 8 cal kyr BP, due to the depleted global ocean alkalinity and/or the variations in surface productivity (at least for MD77‐191).