The Southern Ocean (SO) connects various ocean basins and hosts large air-sea carbon fluxes due to high primary productivity facilitated by resurfacing of deep nutrient-rich waters by strong surface winds. Vertical mixing, induced by breaking waves excited by strong surface winds and interaction of jets and eddies with rough topography, has been considered of secondary importance for the global meridional overturning circulation. Its importance for biological cycles has largely been assumed to be due to the role of mixing in changing the underlying dynamics on centennial timescale. Using an eddy-resolving ocean model that assimilates an extensive array of observations we show that ‘unaccounted for’ mixing in the top few hundred meters can lead to up to 60% change in SO air-sea fluxes in only a few years through altering the distribution of Dissolved Inorganic Carbon, alkalinity, temperature and salinity. Such mixing is induced by propagation of tidal waves from around the globe to the SO as well as flux of wave energy from the deep SO to shallow depths. Such processes are unresolved in climate models, yet essential.