These data are part of the measurements conducted at the time series station Boknis Eck located in the southwestern Baltic Sea at 54°31.77'N, 10°02.36'E. The data include dissolved organic carbon (DOC), total dissolved nitrogen (TDN), dissolved organic nitrogen (DON), bacterial biomes production and bacterial cell counts. Samples were taken once a month at 6 standard depths (1, 5, 10, 15, 20 and 25 m). The data was acquired onboard FK Littorina using a rosette sampler. DOC/TDN were measured using a TOC analyzer, bacterial biomass production data was acquired by leucine incorporation (70 min incubation and counted using a liquid scintillation counter), and bacterial cell abundance was determined using flow cytometry.