Subantarctic Mode Water (SAMW) in the Pacific forms in two distinct pools in the south central and southeast Pacific, which subduct into the ocean interior and impact global storage of heat and carbon. Wintertime thickness of the central and eastern SAMW pools vary predominantly out of phase with each other, by up to ±150 m between years, resulting in an interannual thickness see‐saw. The thickness in the eastern (central) pool is found to be strongly positively (negatively) correlated with both the Southern Annular Mode (SAM) and El Niño–Southern Oscillation (ENSO). The relative phases of the SAM and ENSO set the SAMW thickness, with in phase reinforcing modes in 2005–2008 and 2012–2017 driving strong differences between the pools. Between 2008 and 2012 out of phase atmospheric modes result in less coherent SAMW patterns. SAMW thickness is dominated by local formation driven by SAM and ENSO modulated wind stress and turbulent heat fluxes. Plain Language Summary The Southern Ocean around Antarctica is a dominant pathway for moving heat and carbon from the atmosphere into the ocean interior, trapping it for hundreds of years. Most of this uptake is achieved through the formation of “mode waters”, homogeneous layers of water several hundred meters thick, by sinking and overturning as surface waters cool in winter. We find that two distinct pools of mode water in the South Pacific vary dramatically in winter thickness and volume from year to year. They vary in opposition to one another; when one is thicker than normal the other is thinner, with the pattern reversing after a year or so. We show that this “see‐saw” in thickness is strongest when the two main atmospheric patterns of climate variability over the Southern Ocean are reinforcing one another and weaken when they oppose one another. The combination of these patterns of atmospheric variability sets local mode water thickness via surface winds and ocean heat loss. The discovery of such strong dependence of mode water heat content on these atmospheric patterns is important for climate. Atmospheric variability is predicted to change into the future, potentially impacting heat uptake by mode waters and influencing global surface temperatures. Key Points South Pacific Subantarctic Mode Water (SAMW) layers display large (±150 m) changes in thickness from year to year Two distinct pools of South Pacific SAMW exist and their thicknesses see‐saw out of phase with one another The phase and magnitude of variability are set by changes in wind stress and heat flux driven by the main atmospheric modes of variability