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We examined trophic positions and fatty acid concentrations of riverine, lacustrine, and aquaculture diet and fish in Austrian pre-alpine aquatic ecosystems. It was hypothesized that dietary fatty acid (FA) profiles largely influence the FA composition of the salmonids Salvelinus alpinus, Salmo trutta, and Oncorhynchus mykiss. We analyzed trophic positions using stable isotopes (δ15N) and tested for correlations with polyunsaturated fatty acid (PUFA) concentrations. Gut content analysis revealed benthos (rivers), pellets (aquaculture), and zooplankton (lakes) as the predominant diet source. Results of dorsal muscle tissues analysis showed that the omega-3 PUFA, docosahexaenoic acid (DHA; 22:6 n − 3), was the mostly retained PUFA in all fish of all ecosystems, yet with the highest concentrations in S. alpinus from aquaculture (mean: 20 mg DHA/g dry weight). Moreover, we found that eicosapentaenoic acid (EPA; 20:5 n − 3) in fish of natural habitats (rivers, lakes) was the second most abundant PUFA (3–5 mg/g DW), whereas aquaculture-raised fish had higher concentrations of the omega-6 linoleic acid (18:2 n – 6; 9–11 mg/g DW) than EPA. In addition, PUFA patterns showed that higher omega-3/-6 ratios in aquacultures than in both riverine and lacustrine fish. Data of this pilot field study suggest that salmonids did not seem to directly adjust their PUFA to dietary PUFA profiles in either natural habitats or aquaculture and that some alterations of PUFA are plausible. Finally, we suggest that trophic positions of these freshwater salmonids do not predict PUFA concentrations in their dorsal muscle tissues. [ABSTRACT FROM AUTHOR]