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Abstract We compare the vertical hydrography of the Community Earth System Model Large Ensemble (CESM1‐LE) with observations from two specific periods: the Arctic Ice Dynamics Joint Experiment (AIDJEX; 1975–1976) and Ice‐Tethered Profilers (ITP; 2004–2018). A comparison between simulated and observed salinity and potential temperature profiles highlights two key model biases in all ensemble members: (a) an absence of Pacific Waters in the water column and (b) a slight deepening of the May mixed layer contrary to observations, which show a large reduction in the mixed‐layer depth and an increase in stratification over the same time period. We examine processes controlling the sea ice mass balance using a one‐dimensional vertical heat budget in the light of the model limitations implied by these two biases. Results indicate that remnant solar heat trapped beneath the halocline is mostly ventilated to the surface by mixing before the following melt season. Furthermore, we find that vertical advection associated with Ekman pumping has only a small effect on the vertical heat transport, even in early fall when the winds are strong and the pack ice is weak. Lastly, we estimate the impact of the missing Pacific Waters at 0.40 m of reduced winter ice growth.