Diet quality is crucial for the development of offspring. Here, we examined how the nutritional quality of prey affects somatic growth and the lipid, carbohydrate, protein, amino acid, and polyunsaturated fatty acid content of rainbow trout (Oncorhynchus mykiss) fry using a three-trophic-level experimental setup. Diets differed especially in their content of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), which are physiologically essential polyunsaturated fatty acids for a fish fry. Trout were fed with an artificial diet (fish feed, DHA-rich), marine zooplankton diet (krill/Mysis, DHA-rich), or freshwater zooplankton diet (Daphnia, Cladocera, DHA-deficient). The Daphnia were grown either on a poor, intermediate, or high-quality algal/microbial diet simulating potential changes in the nutritional prey quality (EPA-content). Trout fed with the fish feed or marine zooplankton entirely replaced their muscle tissue composition with compounds of dietary origin. In contrast, fish tissue renewal was only partial in fish fed any Daphnia diet. Furthermore, fish grew five times faster on marine zooplankton than on any of the Daphnia diets. This was mainly explained by the higher dietary contents of arachidonic acid (ARA), EPA, and DHA, but also by the higher content of some amino acids in the marine zooplankton than in the Daphnia diets. Moreover, fatty acid-specific carbon isotopes revealed that trout fry could not biosynthesize ARA, EPA, or DHA efficiently from their precursors. Our results suggest that changes in the zooplankton and macroinvertebrate communities' structure in freshwater habitats from DHA-rich to DHA-poor species may reduce the somatic growth of fish fry.