We investigate the multidecadal and decadal trends in the flux of CO2 between the atmosphere and the Southern Ocean using output from hindcast simulations of an ocean circulation model with embedded biogeochemistry. The simulations are run with NCEP-1 forcing under both preindustrial and historical atmospheric CO2 concentrations so that we can separately analyze trends in the natural and anthropogenic CO2 fluxes. We find that the Southern Ocean (<35°S) CO2 sink has weakened by 0.1 Pg C a−1 from 1979–2004, relative to the expected sink from rising atmospheric CO2 and fixed physical climate. Although the magnitude of this trend is in agreement with prior studies (Le Quéré et al., 2007), its size may not be entirely robust because of uncertainties associated with the trend in the NCEP-1 atmospheric forcing. We attribute the weakening sink to an outgassing trend of natural CO2, driven by enhanced upwelling and equatorward transport of carbon-rich water, which are caused by a trend toward stronger and southward shifted winds over the Southern Ocean (associated with the positive trend in the Southern Annular Mode (SAM)). In contrast, the trend in the anthropogenic CO2 uptake is largely unaffected by the trend in the wind and ocean circulation. We regard this attribution of the trend as robust, and show that surface and interior ocean observations may help to solidify our findings. As coupled climate models consistently show a positive trend in the SAM in the coming century [e.g., Meehl et al., 2007], these mechanistic results are useful for projecting the future behavior of the Southern Ocean carbon sink.