We analyzed the taxonomic and fatty-acid (FA) compositions of phytoplankton and zooplankton, and the environmental conditions at three coastal and offshore stations of the northern Baltic Sea. Plankton samples for FA analyses were collected under the framework of sampling campaigns of the Swedish National Marine Monitoring program in September 2017. Monitoring data of phytoplankton and zooplankton biomass, and environmental variables at each station were extracted from the Swedish Meteorological and Hydrological Institute database (https://sharkweb.smhi.se/). Monthly phytoplankton biomass at each station in July-September 2017 was aggregated by class (i.e., chyrsophytes, cryptophytes, dinoflagellates, diatoms, euglenophytes, cyanobacteria, etc.). Zooplankton biomass in September 2017 was aggregated by major taxa (i.e., sp. [Calanoida], [Calanoida], Cladocera, and other copepods (i.e. excluding and )). Environmental variables monthly monitored in January-October 2017 included salinity, concentrations of dissolved organic carbon, humic substances, total nitrogen and total phosphorus. These variables were measured from 0 to 10 m depth below water surface, and the depth-integrated averages were used for data analyses. Seston and zooplankton ( sp. and Cladocera) FA compositions were analyzed using gas chromatography and mass spectroscopy (GC-MS). Our dataset could provide new insights into how taxonomic composition and biochemical quality of the planktonic food chains change with the environmental conditions in subarctic marine ecosystems.