Monthly sampling at the Boknis Eck (BE) Time Series Station started on 30 April 1957 and, thus, BE represents one of the oldest continuously sampled marine time series sites worldwide. The long high-quality time series observations at BE are invaluable to decipher long-term trends in a representative coastal environment, which is locally (via eutrophication) and globally (via climate change) influenced by human activities. The location of BE at the entrance of the Eckernförde Bay (SW Baltic Sea) makes it an ideal site (i) to study a coastal ecosystem under the influence of pronounced changes of salinity and (ii) to study biogeochemical processes sensitive to pronounced changes of dissolved oxygen (i.e. hypoxia/anoxia). This special issue of Biogeosciences (BG) aims to bring together papers which cover different topics (eutrophication, deoxygenation, trace gas production, nitrogen cycling, marine microbiology) and approaches (incl. measurements and model studies) in order to investigate the biogeochemical processes in the water column and in the sediments at BE and the SW Baltic Sea. You are welcome to submit manuscripts on related topics to this special issue of BG.