Research on per- and polyfluoroalkyl substances (PFAS) in freshwater ecosystems has focused primarily on legacy compounds and little is still known on the presence of emerging PFAS. Here, we investigated the occurrence of 60 anionic, zwitterionic, and cationic PFAS in a food web of the St. Lawrence River (Quebec, Canada) near a major metropolitan area. Water, sediments, aquatic vegetation, invertebrates, and 14 fish species were targeted for analysis. Levels of perfluorobutanoic acid (PFBA) in river water exceeded those of perfluorooctanoic acid (PFOA) or perfluorooctane sulfonate (PFOS), and a zwitterionic betaine was observed for the first time in the St. Lawrence River. The highest mean PFAS concentrations were observed for the benthopelagic top predator Smallmouth bass (Micropterus dolomieu, Σ60PFAS ∼ 92 ± 34 ng/g wet weight whole-body) and the lowest for aquatic plants (0.52–2.3 ng/g). Up to 33 PFAS were detected in biotic samples, with frequent occurrences of emerging PFAS such as perfluorobutane sulfonamide (FBSA) and perfluoroethyl cyclohexane sulfonate (PFECHS), while targeted ether-PFAS all remained undetected. PFOS and long-chain perfluorocarboxylates (C10–C13 PFCAs) dominated the contamination profiles in biota except for insects where PFBA was predominant. Gammarids, molluscs, and insects also had frequent detections of PFOA and fluorotelomer sulfonates, an important distinction with fish and presumably due to different metabolism. Based on bioaccumulation factors >5000 and trophic magnification factors >1, long-chain (C10–C13) PFCAs, PFOS, perfluorodecane sulfonate, and perfluorooctane sulfonamide qualified as very bioaccumulative and biomagnifying. Newly monitored PFAS such as FBSA and PFECHS were biomagnified but moderately bioaccumulative, while PFOA was biodiluted.