The Baltic Sea, which is surrounded by countries with intensive industrial and agricultural activities, is affected by an excess of nitrogen causing large-scale eutrophication. Thus, the nitrogen cycle of the Baltic Sea has received considerable attention over the past five decades mainly due to the ongoing expansion of oxygen-free zones (anoxia), which was identified as a major threat already in the 1970s. Measures to reduce eutrophication have resulted in a decrease of nitrogen inputs since the 1980s, but the environmental status of the Baltic Sea is still far from good. The nitrogen cycle of the Baltic Sea is driven by various microbial processes, which occur to varying extent in both the water column and sediments under oxic and anoxic conditions. However, the overall nitrogen budget of the Baltic Sea is mainly controlled by microbial nitrogen fixation and denitrification in combination with riverine input, aerosol deposition, burial in sediments, and exchange with the North Sea. Other contributors to the nitrogen budget are minor, such as nitrous oxide emissions, or still uncertain, such as submarine groundwater discharge. In general, nitrogen flux estimates are associated with a high degree of uncertainties largely due to inadequate seasonal and spatial coverage of most measurements. To address the existing knowledge gaps and to decipher the processes and fluxes of the Baltic Sea’s nitrogen cycle in the 21<sup>st</sup> century, we suggest establishing time-series measurements and joint process studies at representative sites in the open and coastal Baltic Sea, including the sea-ice covered areas. These studies should combine microbial, molecular, ecological and biogeochemical methods across nano- to kilometre scales to obtain a better understanding of the process rates, their controlling factors and the microbial communities involved. Such results will help to improve physical, biogeochemical and ecosystem models and allow us to reduce the uncertainties in projections of the future nitrogen cycle of the Baltic Sea which can advance/help management measures for ecosystem restoration.