The rate of decline in regulated persistent organic pollutant (POP) concentrations in Baltic Sea biota has leveled off in recent years, with new contaminants frequently being discovered. There is, therefore, a need for comprehensive approaches to study occurrence and temporal trends of a wide range of environmental contaminants, including legacy POPs, contaminants of emerging concern (CECs), and new contaminants. In the current work, non-target screening (NTS) workflows were developed and used for, to the best of our knowledge, the first time-trend directed NTS of biota using gas chromatography–high-resolution mass spectrometry (GC-HRMS). To maximize contaminant coverage, both electron ionization (EI) and electron capture negative ion chemical ionization (ECNI) were used. The EI data were treated using highly automated workflows to find, prioritize, and tentatively identify contaminants with statistically significant temporal trends. The ECNI data were manually processed and reviewed prior to time-trend analysis. Altogether, more than 300 tentatively identified contaminants were found to have significant temporal trends in samples of Baltic guillemot, harbor porpoise, or white-tailed sea eagle. Significant decreases were found for many regulated chemicals, as could be expected, such as PCBs, polychlorinated terphenyls, chlorobenzenes, toxaphenes, DDT, other organochlorine pesticides, and tri- and tetra- bromodiphenyl ethers (BDEs). The rate of decline of legacy POPs agreed well with data reported from targeted analyses. Significant increases were observed for small polycyclic aromatic hydrocarbons, heptaBDEs, CECs, and terpenes and related compounds. The CECs included, among others, one plasticizer tributyl acetylcitrate (ATBC), two antioxidants 2,6-bis(1,1-dimethylethyl)phenol and 2,6-bis(tert-butyl)-4-(4-morpholinyl-methyl)phenol, and two compounds used in polymer production, trimethyl isocyanurate and 2-mercaptobenzothiazole, which had not previously been reported in biota. Their increased concentrations in biota indicate increased use and release. The increase in ATBC may be linked to increased use of it as a substitute for di-2-ethylhexyl phthalate (DEHP), which has been phased out over the last decade.