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Oxygen depletion in the 100‐m thick bottom layer of the deep Lower St. Lawrence Estuary is currently thought to be principally caused by benthic oxygen demand overcoming turbulent oxygenation from overlying layers, with pelagic respiration playing a secondary role. This conception is revisited with idealized numerical simulations, historical oxygen observations and new turbulence measurements. Results indicate that a dominant sediment oxygen demand, over pelagic, is incompatible with the shape of observed oxygen profiles. It is further argued that to sustain oxygen depletion, the turbulent diffusivity in the bottom waters should be ≪10⁻⁴ m² s⁻¹, consistent with direct measurements but contrary to previous model results. A new model that includes an Arrhenius‐type function for pelagic respiration and a parameterization for turbulence diffusivity is developed. The model demonstrates the importance of the …