Salmoniformes are valuable commercial fish that are high in physiologically important omega-3 long-chain polyunsaturated fatty acids (LC-PUFAs), namely eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic (DHA; 22:6n-3) ones. The content of EPA and DHA and, as a result, the quality of fish for consumers depend on the fish diet. We studied the fatty acid (FA) content and composition of grayling, Thymallus baicalensis, inhabiting six rivers, which differed in food supply for fish. The diet of fish was studied using fatty acid markers in adipose tissue and stomach content. In two rivers, grayling's diet was of aquatic origin, while in four rivers, terrestrial invertebrates constituted a high proportion of the fish diet. The study was conducted to test the following question: How do diets with varying amounts of terrestrial-based food influence the content of EPA and DHA, as well as the fatty acid composition, in various tissues of grayling? Grayling inhabiting shaded rivers had lower nutritional value as a source of LC-PUFAs for consumers compared to those in unshaded rivers. This was reflected in the diets of grayling in shaded rivers, which included more prey relying on terrestrial sources of FAs compared to unshaded rivers, where dietary items relied on autochthonous production. Furthermore, these different diets greatly affected the content of EPA and DHA in muscle and adipose tissue but demonstrated a less significant impact on PUFA content in the brain. These findings are of interest because they suggest that the nutritional value of grayling tissues, consumed by predators, including humans, depends on source material within a river and adjacent terrestrial habitat.