While new chemicals have replaced major toxic legacy contaminants such as polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDT), knowledge of their current levels and biomagnification potential in Baltic Sea biota is lacking. Therefore, a suite of chemicals of emerging concern, including organophosphate esters (OPEs), short-chain, medium-chain and long-chain chlorinated paraffins (SCCPs, MCCPs, LCCPs), halogenated flame retardants (HFRs), and per- and polyfluoroalkyl substances (PFAS), were analysed in blue mussel (Mytilus edulis), viviparous eelpout (Zoarces viviparus), Atlantic herring (Clupea harengus), grey seal (Halichoerus grypus), harbor seal (Phoca vitulina), harbor porpoise (Phocoena phocoena), common eider (Somateria mollissima), common guillemot (Uria aalge) and white-tailed eagle (Haliaeetus albicilla) from the Baltic Proper, sampled between 2006 and 2016. Results were benchmarked with existing data for legacy contaminants. The mean concentrations for ΣOPEs ranged from 57 to 550 ng g^-1 lipid weight (lw), for ΣCPs from 110 to 640 ng g^-1 lw for ΣHFRs from 0.42 to 80 ng g^-1 lw, and for ΣPFAS from 1.1 to 450 ng g^-1 wet weight. Perfluoro-4-ethylcyclohexanesulfonate (PFECHS) was detected in most species. Levels of OPEs, CPs and HFRs were generally similar or higher than those of polybrominated diphenyl ethers (PBDEs) and/or hexabromocyclododecane (HBCDD). OPE, CP and HFR concentrations were also similar to PCBs and DDTs in blue mussel, viviparous eelpout and Atlantic herring. In marine mammals and birds, PCB and DDT concentrations remained orders of magnitude higher than those of OPEs, CPs, HFRs and PFAS. Predator-prey ratios for individual OPEs (0.28-3.9) and CPs (0.40-5.0) were similar or somewhat lower than those seen for BDE-47 (5.0-29) and HBCDD (2.4-13). Ratios for individual HFRs (0.010-37) and PFAS (0.15-47) were, however, of the same order of magnitude as seen for p,p'-DDE (4.7-66) and CB-153 (31-190), indicating biomagnification potential for many of the emerging contaminants. Lack of toxicity data, including for complex mixtures, makes it difficult to assess the risks emerging contaminants pose. Their occurence and biomagnification potential should trigger risk management measures, particularly for MCCPs, HFRs and PFAS.

In the 1960s, the Baltic Sea was severely polluted by organic contaminants such as PCBs, HCHs, HCB, and DDTs. Elevated concentrations caused severe adverse effects in Baltic biota. Since then, these substances have been monitored temporally and spatially in Baltic biota, primarily in herring (Clupea harengus) and in guillemot (Uria aalge) egg, but also in cod (Gadus morhua), perch (Perca fluviatilis), eelpout (Zoarces viviparous), and blue mussel (Mytilus edulis). These chemicals were banned in Sweden in the late 1970s/early 1980s. Since the start of monitoring, overall significant decreases of about 70–90 % have been observed. However, concentrations are still higher in the Baltic Sea than in, for example, the North Sea. CB-118 and DDE exceed the suggested target concentrations (24 µg kg⁻¹ lipid weight and 5 µg kg⁻¹ wet weight, respectively) at certain sites in some of the monitored species, showing that concentrations may still be too high to protect the most sensitive organisms.

Polychlorinated biphenyls (PCBs) have been monitored in perch (Perca fluviatilis), pike (Esox lucius), and Arctic char (Salvelinus alpinus) in reference lakes since the late 1960s. Temporal trends and spatial patterns are currently monitored in nine and 32 lakes, respectively. Overall, PCB concentrations are decreasing. However, this is not consistent for all congeners across all lakes and species. Perch has comparatively low PCB concentrations relative to suggested target levels, but individual congener concentrations in some lakes are concerningly high. No temporal trend is seen for CB-118 and CB-153 in perch, but significant decreasing trends exist for Arctic char and pike, for which monitoring started earlier than for perch. The lower/higher chlorinated congener ratio decreased over time in most lakes, indicating fewer new emissions. CB-118 and CB-153 concentrations in perch show spatial gradients across Sweden, with higher concentrations found near urban/industrial areas.

Widespread persistent contaminants are a global environmental problem. In the Baltic Sea, wildlife contamination was first noticed in the 1960s, prompting the Swedish Environmental Protection Agency to establish a comprehensive Swedish National Monitoring Programme for Contaminants in Marine Biota (MCoM) in 1978 run by the Swedish Museum of Natural History. Eight species have been analysed, four fish species (Atlantic herring, Atlantic cod, European perch, viviparous eelpout), one bivalve species (blue mussel), and egg from three bird species (common guillemot, common tern, Eurasian oystercatcher). Here, we present a dataset containing MCoM data from its start until 2021. It includes 36 sets of time-series, each analysed for more than 100 contaminants. The longest time-series is for common guillemot and starts in 1968. We describe the structure of MCoM including historic changes to the number of stations, sample treatment, analytical methods, instruments, and laboratories. The MCoM data is available at the Bolin Centre repository and on GitHub through our R package mcomDb. The latter will be updated yearly with new MCoM records.

Blue mussels are a target species in contaminant monitoring regarding Polycyclic Aromatic Hydrocarbons (PAHs) in biota, and also used as an isotope baseline for trophic position assessment in other biota. The latter is crucial for calculating biomagnification potential of environmental contaminants. This data set comprises long-term time series of PAHs (15 individual substances) in Baltic Sea blue mussels (Mytilus trossulus edulis) from Kvädöfjärden (collected from a depth of 5–10 m), a reference area along the Swedish coast in the Baltic Proper from 25 years during 1987–2016, and of stable isotopes in five individuals (2 cm mussels) per year during the time period 1981–2017. The data has been co-analysed with environmental (oceanographic) data in “The importance of adjusting contaminant concentrations using environmental data: a retrospective study of 25 years data in Baltic blue mussels” published in: Science of the Total Environment (https://doi.org/10.1016/j.scitotenv.2020.143913).