1. Although parasites are expected to affect their host’s fitness, quantitative proof for impacts of parasitism on wild populations is hampered by confounding environmental factors, including dietary resource. 2. Herein, we evaluate whether the physiological conditions of European perch (Perca fluviatilis) in three large peri-alpine lakes (Geneva, Annecy, and Bourget) depend on (a) the nutritional status of the juvenile fish, as revealed by stable isotope and fatty acid compositions, (b) the prevalence of the tapeworm Triaenophorus nodulosus, a parasite transmitted to perch through copepod preys, or (c) interactive effects of both factors. 3. At the scale of lake populations, the deficit in growth and fat storage of juvenile perch during their first summer coincides with a high parasite prevalence and also a low quality of dietary resource. 4. Yet, at the individual level, parasites had no evident effect on the growth of the juvenile perch, while impacts on fat storage appeared only at the highest prevalence of the most infected lake. Fatty acid and stable isotope analyses of fish tissue do not reveal any impact of T. nodulosus on diet, physiology, and feeding behaviour of fish within lakes. 5. Overall, we found a low impact of parasitism on the physiological condition and trophic status of juvenile perch at the end of their first summer. We find instead that juvenile perch growth and fat storage, both factors tied to their winter survival, are under strong nutritional constraints. 6. However, the coinciding nutritional constraints and parasite prevalence of perch juveniles in these three lakes may result from the indirect effect of lake nutrient concentrations, which, as a major control of zooplankton communities, simultaneously regulate both the dietary quality of fish prey and the host–parasite encounter rates.