The increase in anthropogenic nitrogen (N) emissions to the environment has led to serious eutrophication in marine ecosystems with increasing oxygen deficient zones (Hypoxia) and more harmful algae blooms. The Baltic Sea, one of the world’s largest brackish water bodies, suffers from eutrophication by large N loads from rivers and oxygen deficiency in the central, deep basins. Therefore studies on the identification of major nitrate sources to the Baltic Sea and on the nitrogen loss and turnover in the hypoxic waters were performed.