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.

Eutrophication of the Baltic Sea has potentially increased the frequency and magnitude of cyanobacteria blooms. Eutrophication leads to increased sedimentation of organic material, increasing the extent of anoxic bottoms and subsequently increasing the internal phosphorus loading. In addition, the hypoxic water volume displays a negative relationship with the total dissolved inorganic nitrogen pool, suggesting greater overall nitrogen removal with increased hypoxia. Enhanced internal loading of phosphorus and the removal of dissolved inorganic nitrogen leads to lower nitrogen to phosphorus ratios, which are one of the main factors promoting nitrogenfixing cyanobacteria blooms. Because cyanobacteria blooms in the open waters of the Baltic Sea seem to be strongly regulated by internal processes, the effects of external nutrient reductions are scale-dependent. During longer time scales, reductions in external phosphorus load may reduce cyanobacteria blooms; however, on shorter time scales the internal phosphorus loading can counteract external phosphorus reductions. The coupled processes inducing internal loading, nitrogen removal, and the prevalence of nitrogen-fixing cyanobacteria can qualitatively be described as a potentially self-sustaining "vicious circle." To effectively reduce cyanobacteria blooms and overall signs of eutrophication, reductions in both nitrogen and phosphorus external loads appear essential.

Deep-water oxygen concentrations in the Baltic Sea are influenced by eutrophication, but also by saltwater inflows from the North Sea. In the last two decades, only two major inflows have been recorded and the lack of major inflows is believed to have resulted in a long-term stagnation of the deepest bottom water. Analyzing data from 1970 to 2000 at the basin scale, we show that the estimated volume of water with oxygen, <2 mL L(-1), was actually at a minimum at the end of the longest so-called stagnation period on record. We also show that annual changes in dissolved inorganic phosphate water pools were positively correlated to the area of bottom covered by hypoxic water, but not to changes in total phosphorus load, thus addressing the legacy of eutrophication on a basinwide scale. The variations in phosphorus pools that have occurred during the past decades do not reflect any human action to reduce inputs. The long residence time and internally controlled variation of the large P pool in the Baltic Sea has important implications for management of both N and P inputs into this eutrophicated enclosed basin.

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Overall budgets for nutrient and humus are described for the Baltic Sea as well as for the subsystems, i.e., the Baltic proper, the Bothnian Bay and the Bothnian Sea. The residence times for total phosphorus, total nitrogen, silicate and humus are 13.3, 5.5, 11.2 and 9.6 years respectively, compared to 21.8 years for a conservative substance (salt). About 90% of the nutrient losses are due to biogeochemical sinks within the Baltic Sea. Thus only about 10% is exported to external areas (the Kattegat/Belt Sea). For humus the corresponding figures are about 75 and 25%, respectively. This means that the Baltic Sea to a large extent can be regarded as a closed system and perturbations in the water exchange with the North Sea should have little effect on the nutrient budgets. The sinks are parameterized by an expression borrowed from limnology where the net nutrient loss is a function of the winter surface concentration. A budget model is run in a prognostic, hindcast mode with the assumed time‐dependent phosphorus and nitrogen loading of the Baltic proper. The computed development of the winter surface concentrations of total P and total N for the period 1950‐1988 appears quite realistic. The possibility of having variable sinks which are functions of the surface winter concentrations of nitrogen and phosphorus is described using calculations based on data from the different Baltic subareas. Such sinks should significantly decrease the winter N:P ratio in the surface water when the nutrient loading increases with time. With better descriptions of in particular the pools of nutrients in the sediment, it would be possible to model future changes of nutrient concentrations in the water column in relation to loading.