The Southern Ocean is the single most important region for the oceanic uptake of atmospheric carbon dioxide, accounting for approximately 40% of the oceanic carbon sink. However, mechanisms controlling the uptake, transport and storage of carbon is not well understood in this region. The extratropical southern hemispheric atmosphere is undergoing significant multi-decadal climate change characterized by the positive trend in the Southern Annular Mode, and its impacts on seaice, air-sea momentum and heat fluxes, and mesoscale eddy fields have been observed. In this presentation, a hierarchy of numerical simulations are used as a tool to understand and quantify the processes controlling the Southern Ocean carbon cycle. Our results points to the importance of coupling between atmospheric climate variability, ocean circulation and marine biogeochemical cycles in regulating the ongoing and future carbon uptake and acidification of the region.