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Arctic amplification has been attributed predominantly to a positive lapse rate feedback in winter, when boundary layer temperature inversions focus warming near the surface. Predicting high-latitude climate change effectively thus requires identifying the local and remote physical processes that set the Arctic’s vertical warming structure. In this study, we analyze output from the CESM Large Ensemble’s twenty-first-century climate change projection to diagnose the relative influence of two Arctic heating sources, local sea ice loss and remote changes in atmospheric heat transport. Causal effects are quantified with a statistical inference method, allowing us to assess the energetic pathways mediating the Arctic temperature response and the role of internal variability across the ensemble. We find that a step-increase in latent heat flux convergence causes Arctic lower-tropospheric warming in all seasons, while additionally reducing net longwave cooling at the surface. However, these effects only lead to small and short-lived changes in boundary layer inversion strength. By contrast, a step-decrease in sea ice extent in the melt season causes, in fall and winter, surface-amplified warming and weakened boundary layer temperature inversions. Sea ice loss also enhances surface turbulent heat fluxes and cloud-driven condensational heating, which mediate the atmospheric temperature response. While the aggregate effect of many moist transport events and seasons of sea ice loss will be different than the response to hypothetical perturbations, our results nonetheless highlight the mechanisms that alter the Arctic temperature inversion in response to CO2 forcing. As sea ice declines, the atmosphere’s boundary layer temperature structure is weakened, static stability decreases, and a thermodynamic coupling emerges between the Arctic surface and the overlying troposphere.