Due to its large heat capacity and circulation, the ocean contributes significantly to global heat uptake, global heat transport, spatial temperature patterns, and variability. Quantifying ocean heat uptake across different temporal and spatial scales is important to quantify Earth's climate response to anthropogenic warming. Here we evaluate ocean adjustment time scales from two different fully coupled climate model ensembles using the Community Earth System Model. Both ensembles use the same model version, anthropogenic and natural forcings, and coupling configurations, but we initialize the ensembles in two different ways: (1) sampling joint internal variability of the ocean–atmosphere system (unique atmosphere and ocean conditions) and (2) sampling the internal variability of the atmosphere only (unique atmosphere, identical ocean conditions). Uncertainty due to internal variability is used as a proxy to quantify the time scales of ocean temperature adjustment at different depths and basins in Community Earth System Model. Time scales of equilibration are longer in the deep ocean than the upper ocean, highlighting the vertical structure of dynamic adjustment. The Atlantic equilibrates on shorter time scales (82 years above 1,000 m, 140 years below 1,000 m) relative to the Pacific (106 years above 1,000 m, 444 years below 1,000 m) in Community Earth System Model due to the large North Atlantic Deep Water formation and strong overturning circulation in the Atlantic. These results have broad implications for analyzing internal climate variability, ocean adjustment, and drift in global coupled model experiments and intercomparisons.