Perfluoroalkyl substances (PFASs) were investigated in filter-feeding shellfish collected from 2013 to 2017 along the English Channel, Atlantic and Mediterranean coasts of France. PFOS (perfluorooctane sulfonate), PFTrDA (perfluorotridecanoic acid), PFTeDA (perfluorotetradecanoic acid), PFDoDA (perfluorododecanoic acid) and PFUnDA (perfluoroundecanoic acid) were detected in more than 80% of samples, thus indicating widespread contamination of the French coastal environment by these chemicals. The distribution of PFAS concentrations showed differences according to sampling locations and years. PFOS was the predominant PFAS in most samples collected from English Channel and Atlantic coasts until 2014, but the opposite was observed in 2015, 2016 and 2017, while perfluoroalkyl carboxylic acids (PFCAs) prevailed in Mediterranean samples in all study years. Among PFCAs, PFTrDA showed the highest maximum (1.36 ng g−1 ww) and median (0.077 ng g−1 ww) concentrations in 2016–2017. Other PFAS median concentrations were within the 0.014 (PFNA) - 0.055 (PFTeDA) ng g−1 ww range. The profiles determined each year in most Mediterranean samples suggest distinctive sources. PFOS median concentrations showed a significant decrease over the study years, from 0.118 to 0.126 ng g−1 ww in 2013–2015 to 0.066 ng g−1 ww in 2016 and 2017. ∑PFCAs showed no trends in concentration ranges over the same years. The shift in PFAS profiles from PFOS to long-chain PFCAs over the study period reflects PFOS production phase-out, combined with continuous inputs of PFCAs into the marine environment. These results provide reference data for future studies of the occurrence of contaminants of emerging concern on European coasts.