Variation in food-chain length may influence a predator’s trophic position. In aquatic food webs, the energy value of prey typically increases with its trophic rank; hence a higher trophic-level diet is often assumed to indicate better habitat quality. We related the body and health condition of pre-fledged Red-necked Grebes Podiceps grisegena to their dietary trophic level (estimated using stable nitrogen isotope signals of feathers) in two managed pond habitats with contrasting prey availability due to different fish population structures. Ponds stocked with young, small common carp Cyprinus carpio provided abundant fish and non-fish (insects and amphibians) resources for chicks. In ponds stocked with large carp, which also supported populations of small predatory fish, the breeding success of grebes was comparatively poor, because carp exceeded the size suitable for chicks and adversely affected non-fish prey. Pre-fledged grebes were in better condition (greater body mass, lower heterophil/lymphocyte ratio) in the food-rich small-fish ponds than in the food-poor ponds dominated by large fish. Values for δ15N suggested shorter food chains and a lower trophic-level diet for grebes in the food-rich ponds. Bayesian carbon and nitrogen isotope mixing models demonstrated the dietary prominence of small fish, both carp and predatory species. Between-habitat differences in food-chain length and grebe trophic position resulted from the higher trophic rank of small predatory fish in the food-poor ponds compared to the omnivorous carp in the food-rich ponds. Our results suggest that in aquatic food webs, feeding at higher trophic levels by strongly size-limited generalist avian predators can be associated with overall food scarcity due to the impact of fish, and thus trophic status cannot be used uncritically as a proxy for aquatic habitat quality.