Large-scale hypoxia is an inherent natural property of the Baltic Sea caused by geographically and climatically determined insufficiency of oxygen supply to the deep water layers. During 1961–2005, the hypoxic zone covered by waters with oxygen concentration less than 2 mL L–1 extended on average over a huge area of about 50,000 km2, albeit with large seasonal (a few thousand km2) and, especially inter-annual (dozens of thousand km2) variations, the later caused by an irregular ventilation with sporadic inflows of saline oxygen-enriched waters. The expansion of hypoxia induces a reduction of dissolved inorganic nitrogen pool due to denitrification and an increase of dissolved phosphate pool by internal loading, these changes reaching hundred thousand tonnes of N and P. The resulting excess of phosphate pool over the “Redfield” demand by phytoplankton is favourable for the dinitrogen fixation by cyanobacteria in amounts sufficient to compensate for denitrification and to counteract possible reductions of the nitrogen land loads