The health of key species in the Baltic region has been impaired by exposure to anthropogenic hazardous substances (AHSs), which accumulate in organisms and are transferred through food chains. There is, thus, a need for comprehensive characterization of the occurrence and accumulation of AHSs in the ecosystem. In this study, we use a non-target screening (NTS) approach for this purpose. A major challenge in NTS of biological samples is the removal of matrix components such as lipids that may interfere with the detection and identification of compounds of interest. Here, we combine gel permeation chromatography with Florisil® column fractionation to achieve sufficient lipid removal for gas chromatography–high-resolution mass spectrometry analysis using electron ionization (EI) and electron capture negative ion chemical ionization (ECNI). In addition, we present new data processing workflows designed to systematically find and identify frequently occurring and biomagnifying AHSs, including known, emerging, and new contaminants. Using these workflows, we discovered a wide range of contaminants in tissue samples from blue mussels, fish, and marine mammals, and calculated their biomagnification factors (BMFs). Compounds with BMFs above 1 for herring and at least one marine mammal included legacy chlorinated pollutants (polychlorinated biphenyls, DDTs, chloro-benzenes/cyclohexanes, chlordanes, toxaphenes, dieldrin), polybrominated diphenyl ethers (PBDEs), and brominated biphenyls. However, there were also several halogenated natural products (halogenated methoxylated brominated diphenyl ethers, 1′-methyl-1,2′-bipyrroles, 1,1′-dimethyl-2,2′-bipyrroles, and the halogenated monoterpene mixed halogenated compound 1) as well as the novel flame retardant Dechlorane 602 and several polycyclic aromatic hydrocarbons, terpenoids, and steroids. The legacy pollutants exhibited the expected biomagnification behavior, demonstrating the utility of the unguided data processing workflow.
