Concentrations in fish of per‐ and polyfluoroalkyl substances (PFAS) were reported for 7 deep lakes in the European subalpine area: Lakes Geneva, Lugano, Maggiore, Iseo, Como, Garda, and Mergozzo; one shallow lowland lake (Varese); and 2 high‐altitude alpine lakes (>2000 m a.s.l). Fillets and, in selected cases, other body fractions (viscera, liver, and residual carcass) from 8 fish species were analyzed. The possibility of harmonizing the monitoring protocols was tested. Results suggest that the sampling season is not critical for PFASs and the total protein content cannot be used for normalization of tissue concentrations because PFASs bind to specific proteins. Moreover, the polar lipid content could be used to reduce the variability of PFAS concentrations in phospholipid rich fractions of fish such as viscera and carcass. The data comparison and analysis show that the PFAS contamination in lake fish is generally correlated with the degree of urbanization of the lake catchment; however, it is sometimes difficult to compare absolute concentrations in lake fish because the lake hydro‐morphological characteristics play a substantial role in determining the chemical concentrations of persistent and mobile contaminants. Environ Toxicol Chem 2021;40:658–676. © 2020 SETAC

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