Lower atmospheric CO2 concentrations during the Last Glacial Maximum (LGM; 23.0‐18.0 ka) have been attributed to the sequestration of respired carbon in the ocean interior, yet the mechanism responsible for the release of this CO2 during the deglaciation remains uncertain. Here, we present calculations of vertical differences in oxygen and carbon isotopes (∆δ18O and ∆δ13C, respectively) from a depth transect of southwest Pacific Ocean sediment cores to reconstruct changes in water mass structure and CO2 storage. During the LGM, ∆δ18O indicates a more homogenous deep Pacific below 1100 m, whereas regional ∆δ13C elucidates greater sequestration of CO2 in two distinct layers: enhanced CO2 storage at intermediate depths between ~940 m and 1400 m, and significantly more CO2 at 1600 m and below. This highlights an isolated glacial intermediate water mass and places the main geochemical divide at least 500 m shallower than the Holocene. During the initial stages of the deglaciation in Heinrich Stadial 1 (HS1; 17.5‐14.5 ka), restructuring of the upper ~2000 m of the southwest Pacific water column coincided with sea‐ice retreat and rapid CO2 release from intermediate depths, while CO2 release in the deep ocean was earlier and more gradual than in the waters above it. These changes suggest that sea ice retreat and shifts in Southern Ocean frontal locations contributed to rapid CO2 ventilation from the Southern Ocean's intermediate depths and gradual ventilation from the deep ocean during the early deglaciation.