Abstract Subantarctic Mode Water (SAMW) plays a vital role in the uptake of heat and carbon, thereby regulating global climate. Mesoscale eddies affect mode‐water subduction and transport in the Southern Ocean. However, it remains unclear how SAMW‐related eddy activity will evolve under anthropogenic warming, because most state‐of‐the‐art climate models do not explicitly resolve mesoscale eddies. Using an eddy‐resolving climate model we explore the evolution of mesoscale eddy activity in SAMW formation regions under global warming, finding that eddy activity exhibits opposite trends, with modest weakening in the Indian Ocean but a marked strengthening in the Pacific. These contrasting responses are linked to projected changes in local wind stress and baroclinic instability. The resulting regional differences drive opposite trends in eddy‐induced vertical transport in SAMW formation regions. Our results demonstrate that regional differences in eddy variability may influence future ocean heat and carbon storage in SAMW.

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