In this study, French marine and freshwater fish perfluoroalkyl acid (PFAA) contamination are presented along with their fatty acid (FA) composition to provide further elements for a risk/benefit balance of fish consumption to be assessed. The 29 most consumed marine fish species were collected in four metropolitan French coastal areas in 2004 to constitute composite samples. Geographical differences in terms of consumed species and contamination level were taken into account. Three hundred and eighty-seven composite samples corresponding to 16 freshwater fish species collected between 2008 and 2010 in the six major French rivers or their tributaries were selected among the French national agency for water and aquatic environments freshwater fish sample library. The raw edible parts were analyzed for FA composition and PFAA contamination. Results show that freshwater fishes are more contaminated by PFAAs than marine fishes and do not share the same contamination profile. Freshwater fish contamination is mostly driven by perfluorooctane sulfonate (PFOS) (7596), whereas marine fish contamination is split between perfluorooctanoic acid (PFOA) (24%), PFOS (20%), perfluorohexanoic acid (PFHxA) (15%), perfluoropentanoic acid (PFHpA) (11%), and perfluorobutanoic acid (PFBA) (1196). Common carp, pike-perch, European perch, thicklip grey mullet, and common roach presented the most unfavorable balance profile due to their high level of PFAAs and low level of n-3 long-chain polyunsaturated fatty acids (LC-PUFAs). These data could be used, if needed, in an updated opinion on fish consumption that takes into account PFAA contamination.