Hypoxia, a growing worldwide problem, has been intermittently present in the modern Baltic Sea since its formation ca. 8000 cal. yr BP. However, both the spatial extent and intensity of hypoxia have increased with anthropogenic eutrophication due to nutrient inputs. Physical processes, which control stratification and the renewal of oxygen in bottom waters, are important constraints on the formation and maintenance of hypoxia. Climate controlled inflows of saline water from the North Sea through the Danish Straits is a critical controlling factor governing the spatial extent and duration of hypoxia. Hypoxia regulates the biogeochemical cycles of both phosphorus (P) and nitrogen (N) in the water column and sediments. Significant amounts of P are currently released from sediments, an order of magnitude larger than anthropogenic inputs. The Baltic Sea is unique for coastal marine ecosystems experiencing N losses in hypoxic waters below the halocline. Although benthic communities in the Baltic Sea are naturally constrained by salinity gradients, hypoxia has resulted in habitat loss over vast areas and the elimination of benthic fauna, and has severely disrupted benthic food webs. Nutrient load reductions are needed to reduce the extent, severity, and effects of hypoxia.

Hypoxia has occurred intermittently over the Holocene in the Baltic Sea, but the recent expansion from less than 10 000 km2 before 1950 to >60 000 km2 since 2000 is mainly caused by enhanced nutrient inputs from land and atmosphere. With worsening hypoxia, the role of sediments changes from nitrogen removal to nitrogen release as ammonium. At present, denitrification in the water column and sediments is equally important. Phosphorus is currently buried in sediments mainly in organic form, with an additional contribution of reduced Fe-phosphate minerals in the deep anoxic basins. Upon the transition to oxic conditions, a significant proportion of the organic phosphorus will be remineralized, with the phosphorus then being bound to iron oxides. This iron-oxide bound phosphorus is readily released to the water column upon the onset of hypoxia again. Important ecosystems services carried out by the benthic fauna, including biogeochemical feedback-loops and biomass production, are also lost with hypoxia. The results provide quantitative knowledge of nutrient release and recycling processes under various environmental conditions in support of decision support tools underlying the Baltic Sea Action Plan.