The reduction of anthropogenic emissions to the Baltic Sea water and adjoined freshwater systems is broadly addressed in the HELCOM conventions, BSAP and EU framework directives. These network activities bring together several ACES units and researchers from Vilnius (Center for Physical Sciences and Technology), Institute of Ecology (Vilnius University, Lithuania), Coastal Research and Planning Institute (Klaipeda University, Lithuania), and Institute of Oceanology (Polish Academy of Sciences, Poland). Our aim is to facilitate mapping of trophic structure of the Baltic ecosystems through the analysis of bulk C, N, and S isotopes. We also investigate the usefulness of isotope analyses of essential and non-essential fatty acids and amino acids as indicators of trophic position and base of the food chain. Ultimately, these data will be used to explain biological responses, trophic magnification factors of contaminants in biota, as well as effects of nutrient and contaminant sources on the spatial differences in marine food webs and in sea-atmospheric transfer.