Background/Question/Methods A combination of abiotic and biotic factors determines species presence, their densities and effects on the ecosystem. However, which factor that is most important can differ between ecosystems. We have studied how predation, competition and habitat structure affect niche overlap in resource utilization in a system of three coexisting stream dwelling species; drift feeding brown trout, benthic stone loach or sculpin, and omnivorous signal crayfish, where adult trout acts as a predator. Previous studies of this system suggest that habitat structure and interactive effects between predation threat and competition affect resource utilization. However, it is not known how species interactions are affected along habitat gradients. In a field study in three different river systems we therefore collected habitat data, fish and crayfish densities together with samples for stable isotopes and gut content. We tested the hypothesis that niche overlap decreases in complex and forested habitats. This is because complex habitats allow for niche differentiation along microhabitat gradients, and because forested habitats allow for terrestrial subsidies, and hence alternative resources, for some species. Furthermore, we expected low densities of intra- and/or interspecific competitors together with low predator densities to decrease niche overlap. Results/Conclusions The results indicate that forested sites and sites with large substrate grain size have lower niche overlap between the three species, but that relative species densities also influence niche width. Thus, habitat characteristics, presence or absence of predators and species interactions, all affect the relative abundance of coexisting species and their resource utilization, which ultimately causes complex patterns in niche overlap not tractable by observing biotic or abiotic interactions in isolation.