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A time-trend study was carried out for two important Baltic Sea species, blue mussel (1994–2017, 11 samples) and eelpout (1994–2017, 11 samples), to track the changes in levels of regulated persistent organic pollutants (POPs) and show potential increases in the levels of the contaminants of emerging concern (CECs). It was carried out utilizing gas chromatography–high-resolution mass spectrometry (GC-HRMS) based non-target screening (NTS). Data were acquired in two modes – electron ionization (EI) and electron capture negative ion chemical ionization (ECNI) – to widen the contaminant coverage, and treated using a fast semi-automated NTS data processing workflow. The study revealed that >250 tentatively identified compounds show statistically significant temporal trends in Baltic blue mussel and eelpout. A large number of regulated substances, including but not limited to PCBs, DDTs and other organochlorine pesticides (OCPs), chlorobenzenes, and many polybrominated diphenyl ethers (PBDEs), showed significant declining trends, as was expected. Their rates of decline were in good agreement with previously reported data. In contrast, increasing trends were observed for many CECs, some polycyclic aromatic compounds (PAHs), and hydrocarbons. The CEC group included, among others, four compounds, namely, one personal care product ingredient, 2-ethylhexyl stearate, one brominated compound 1,2,3,5-tetrabromobenzene and two intermediates 4-isopropoxyaniline and bilobol dimethyl ether, that were reported in marine biota for the first time to the best of our knowledge. Several compounds, including four CECs and two unknown brominated compounds, showed levels considerably higher than the common legacy pollutants (CB-153 and BDE-99), which might be taken into consideration for future monitoring and risk assessment. In addition, this work revealed the presence of a plethora of organoiodinated compounds that exhibited statistically significant temporal trends in the samples under study, which could be of future interest.