In large rivers, fish ontogenic development success is mainly influenced by resource availability and by the possibility of species to adapt their diet (i.e. trophic niche). Humans have drastically modified freshwater habitats, notably for navigation purposes. Such modifications may reduce food availability for young of the year (YOY) fish and, consequently, influence their ability to reach the adult age. In the Meuse River, decrease of fish abundance is thought to be linked to a drastic reduction of phytoplankton biomass. In this context of decreasing phytoplankton biomass, we studied trophic niches of three cyprinid species (common bleak Alburnus alburnus, chub Squalius cephalus, and roach Rutilus rutilus) and one percid species (European perch Perca fluviatilis) at various stages of development, using stable isotope analysis in order to compare intra- and interspecific competition between sites differing in degree of channelisation. Two reaches of the Meuse River differing by their degree of regulation were investigated. We hypothesised that habitat homogenisation would (1) decrease food resource availability and diversity and (2) increase trophic competition, particularly among earlier ontogenic stages, and promote individual specialisation. Our study provides evidence that in the context of low planktonic biomass, most YOY relied on benthic food sources. Furthermore, the Meuse River flow and depth regulation significantly impacted the abundance and species richness of YOY. In the heavily channelised reach, between-stages competition and low resource diversity lead to an increase in diet partitioning between cyprinid larvae, as well as consumption of non-optimal energetic food sources such as aquatic vegetation by some individuals. By contrast, in the less channelised reach, larvae displayed a generalist feeding habit focusing on high energy content prey such as different taxa of macroinvertebrates, suggesting that the diversity of habitat reduces the food competition within and between stages. Intraspecific resource repartition is a key point for YOY fish having to cope with plankton-depleted conditions. Younger cyprinid stages seem more affected by intra- and inter-specific competition in the more channelised reach. YOY fish communities were also less diversified and abundant in the more altered site, which highlight the importance of limiting channelisation to better conserve fish communities.