AbstractWe compare depth and temporal distributions of sub‐fossil assemblages of two cold‐water scleractinian corals on seamounts in the Southwest Pacific to help define the temporal variations of water mass properties in the Southern Ocean (SO) during deglaciation. Peaks in the deep‐water abundance of the two species complement one another, with Desmophyllum dianthus peaking around the Antarctic Cold Reversal (ACR), and Solenosmilia variabilis briefly during the late Heinrich Stadial 1 (HS1) and during the Younger Dryas (YD). Environmental tolerances of the two species and the geochemistry of S. variabilis carbonate skeletons suggest that their secular distributions reflect complementary effects of temperature (higher at Antarctic Intermediate Water/Upper Circumpolar Deep Water depths during the YD and late HS1) and surface productivity (lower during the YD and HS1). Higher temperatures at depth we interpret as evidence of increased Zonal West Wind (ZWW)‐driven Ekman pumping during the late HS1 and YD, whereas coeval low surface production reflects poleward expansion of sub‐tropical water masses as a result of correlated poleward shifts of the ZWW belt and the Intertropical Convergence Zone. More broadly, a continuous deep coral population in the southwest Pacific that spans two species and three deglacial periods (HS1, ACR and the YD) and an early Holocene shift in coral distribution from deeper to shallower habitats appear to reflect large‐scale changes during deglaciation in SO temperature profiles and productivity.