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Abstract The mixed layer of polynyas is vital for local climate as it determines the exchange of properties and energy between ocean, sea ice, and atmosphere. However, its evolution is poorly understood, as it is controlled by complex interactions among these components, yet highly undersampled, especially outside summer. Here, we present a 2-month, high vertical-resolution, full-depth hydrographic dataset from the southeastern Amundsen Sea polynya in austral autumn (from mid-February to mid-April 2014) collected by a recovered seal tag. This novel dataset quantifies the changes in upper-ocean temperature and salinity stratification in this previously unobserved season. Our seal-tag measurements reveal that the mixed layer experiences deepening, salinification, and intense heat loss through surface fluxes. Heat and salt budgets suggest a sea ice formation rate of ∼3 cm per day. We use a one-dimensional model to reproduce the mixed layer evolution and further identify key controls on its characteristics. Our experiments with a range of reduced or amplified air–sea fluxes show that heat loss to the atmosphere and related sea ice formation are the principal determinants of stratification evolution. Additionally, our modeling demonstrates that horizontal advection is required to fully explain the mixed layer evolution, underlining the importance of the ice-covered neighboring region for determining sea ice formation rates in the Amundsen Sea polynya. Our findings suggest that the potential overestimation of sea ice production by satellite-based methods, due to the absence of oceanic heat flux, could be offset by horizontal advection inhibiting mixed layer deepening and sustaining sea ice formation.