Temporal and spatial trends of perfluoroalkyl acids (PFAAs) were investigated in Baltic Sea herring liver (Clupea harengus) from three sites, and white-tailed sea eagle (WTSE) eggs (Haliaeetus albicilla) from two freshwater and two marine areas in Sweden. Trends of most quantifiable PFAAs increased over the monitored period (1980-2014 in herring, 1960s/1980s-2010 in WTSE). No significant decreasing trends were observed for the most recent ten years for any substances, except perfluorooctane sulfonamide (FOSA). Concentrations of perfluorooctanesulfonic acids (PFOS) in herring showed a distinct decreasing spatial trend moving from the more southern site toward the more northern site, indicating main input of PFOS into the southern Baltic Sea. For WTSE, PFOS concentration was higher in the marine compared to the freshwater environment, explained by the cumulative historic contamination of the Baltic Sea. Similarly, concentrations in WTSE were lower in the northern part of the Baltic Sea compared to further south. Concentrations of PFUnDA, representing long-chain perfluoroalkyl carboxylic acids (PFCAs), showed a more homogeneous spatial distribution compared to PFOS for both herring and WTSE, indicating that atmospheric inputs (via precursors) of the long-chain PFCAs are important contributors in the study areas.