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We investigated the dissolved oxygen metabolism of the Curonian Lagoon (Baltic Sea) to assess the relative contributions of pelagic and benthic processes to the development of transient hypoxic conditions in shallow water habitats. Metabolism measurements along with the remote sensing-derived estimates of spatial variability in chlorophyll a were used to evaluate the risk of hypoxia at the whole lagoon level. Our data demonstrate that cyanobacterial blooms strongly inhibit light penetration, resulting in net heterotrophic conditions in which pelagic oxygen demand exceeds benthic oxygen demand by an order of magnitude. The combination of bloom conditions and reduced vertical mixing during calm periods resulted in oxygen depletion of bottom waters and greater sediment nutrient release. The peak of reactive P regeneration (nearly 30 μmol m⁻² h⁻¹) coincided with oxygen depletion in the water …