AbstractBackground subsurface vertical mixing rates in the Southern Ocean (SO) are known to vary by an order of magnitude temporally and spatially, due to variability in their generating mechanisms, which include winds and shear instabilities at the surface, and the interaction of tides and lee waves with rough bottom topography. There is great uncertainty in the parameterization of this mixing in coarse resolution Earth System Models (ESM), and in the impact that this has on SO biological productivity on sub decadal timescales. Using a data assimilating biogeochemical ocean model we show that SO phytoplankton productivity is highly sensitive to differences in background diapycnal mixing over short timescales. Changes in the background vertical mixing rates alter key biogeochemical and physical conditions. The greatest changes to the distribution of physical and biogeochemical tracers occur in regions with very strong tracer vertical gradients. A combination of reduced nutrient limitation and reduced light limitation causes a strong increase in SO phytoplankton productivity with higher background mixing. This leads to increased summer carbon export but reduced wintertime export over the mixed layer depth, which could alter the strength of the SO biological carbon pump and atmospheric concentrations on centennial to millennial timescales. This study demonstrates the importance of accurately representing diapycnal mixing in ESM to predict SO biogeochemical dynamics and their broader climatic implications.