Anthropogenic CO$_2$ emission-induced feedbacks between the carbon cycle and the climate system perturb the efficiency of atmospheric CO$_2$ uptake by land and ocean carbon reservoirs. The Southern Ocean is a region where these feedbacks can be largest and differ most among Earth System Model projections of 21st century climate change. To improve our mechanistic understanding of these feedbacks, we develop an automated procedure that tracks changes in the positions of Southern Ocean water masses and their carbon uptake. In an idealised ensemble of climate change projections, we diagnose two carbon–concentration feedbacks driven by atmospheric CO$_2$ (due to increasing air-sea CO$_2$ partial pressure difference, dpCO$_2$ , and reducing carbonate buffering capacity) and two carbon–climate feedbacks driven by climate change (due to changes in the water mass surface outcrop areas and local climate impacts). Collectively these feedbacks increase the CO$_2$ uptake by the Southern Ocean and account for one-fifth of the global uptake of CO$_2$ emissions. The increase in CO$_2$ uptake is primarily dpCO$_2$ -driven, with Antarctic intermediate waters making the largest contribution; the remaining three feedbacks partially offset this increase (by ~25%), with maximum reductions in Subantarctic mode waters. The process dominating the decrease in CO$_2$ uptake is water mass-dependent: reduction in carbonate buffering capacity in Subtropical and Subantarctic mode waters, local climate impacts in Antarctic intermediate waters, and reduction in outcrop areas in circumpolar deep waters and Antarctic bottom waters. Intermodel variability in the feedbacks is predominately dpCO$_2$ –driven and should be a focus of efforts to constrain projection uncertainty.