Abstract. Estimates of the ocean's large-scale transport of anthropogenic CO₂ are based on one-time hydrographic sections, but the temporal variability of this transport has not been investigated. The aim of this study is to evaluate how the seasonal and mesoscale variability affect data-based estimates of anthropogenic CO₂ transport. To diagnose this variability, we made a global anthropogenic CO₂ simulation using an eddy-permitting version of the coupled ocean sea-ice model ORCA-LIM. As for heat transport, the seasonally varying transport of anthropogenic CO₂ is largest within 20° of the equator and shows secondary maxima in the subtropics. Ekman transport generally drives most of the seasonal variability, but the contribution of the vertical shear becomes important near the equator and in the Southern Ocean. Mesoscale variabilty contributes to the annual-mean transport of both heat and anthropogenic CO₂ with strong poleward transport in the Southern Ocean and equatorward transport in the tropics. This "rectified" eddy transport is largely baroclinic in the tropics and barotropic in the Southern Ocean due to a larger contribution from standing eddies. Our analysis revealed that most previous hydrographic estimates of meridional transport of anthropogenic CO₂ are severely biased because they neglect temporal fluctuations due to non-Ekman velocity variations. In each of the three major ocean basins, this bias is largest near the equator and in the high southern latitudes. In the subtropical North Atlantic, where most of the hydrographic-based estimates have been focused, this uncertainty represents up to 20% and 30% of total meridional transport of heat and CO₂. Generally though, outside the tropics and Southern Ocean, there are only small variations in meridional transport due to seasonal variations in tracer fields and time variations in eddy transport. For the North Atlantic, eddy variability accounts for up to 10% and 15% of the total transport of heat and CO₂. This component is not accounted for in coarse-resolution hydrographic surveys.