A combined method for quantitative analysis, along with suspect and non-target screening of per- and polyfluoroalkyl substances (PFAS) was developed using ultra-high pressure liquid chromatography-ultra-high resolution (Orbitrap) mass spectrometry. The method was applied together with measurements of total- and extractable organofluorine (TF and EOF, respectively), to pooled serum samples from 1996–2017 from first-time mothers living in the county of Uppsala, Sweden, some of which (i.e. 148 of 472 women sampled 1996–2012) were exposed to drinking water contaminated with perfluorohexane sulfonate (PFHxS) and other PFAS until mid-2012. Declining trends were observed for all target PFAS as well as TF, with homologue-dependent differences in year of onset of decline. Only 33% of samples displayed detectable EOF, and amongst these samples the percentage of EOF explained by target PFAS declined significantly (−3.5% per year) over the entire study period. This finding corroborates prior observations in Germany after the year 2000, and may reflect increasing exposure to novel PFAS which have not yet been identified. Suspect screening revealed the presence of perfluoro-4-ethylcyclohexanesulfonate (PFECHS), which displayed declining trends since the year 2000. Non-target time trend screening revealed 3 unidentified features with time trends matching PFHxS. These features require further investigation, but may represent contaminants which co-occurred with PFHxS in the contaminated drinking water.