1. Generalist fish species are recognised as important couplers of benthic and pelagic food-web compartments in lakes. However, interspecific niche segregation and individual specialisation may limit the potential for generalistic feeding behaviour.
2. We studied summer habitat use, stomach contents and stable isotopic compositions of the generalist feeder Arctic charr coexisting with its common resource competitor brown trout in five subarctic lakes in northern Norway to reveal population-level and individual-level niche plasticity.
3. Charr and trout showed partial niche segregation in all five lakes. Charr used all habitat types and a wide variety of invertebrate prey including zooplankton, whereas trout fed mainly on insects in the littoral zone. Hence, charr showed a higher potential to promote habitat and food-web coupling compared to littoral-dwelling trout.
4. The level of niche segregation between charr and trout and between pelagic-caught and littoral-caught charr depended on the prevailing patterns of interspecific and intraspecific resource competition. The two fish species had partially overlapping trophic niches in one lake where charr numerically dominated the fish community, whereas the most segregated niches occurred in lakes where trout were more abundant.
5. In general, pelagic-caught charr had substantially narrower dietary and isotopic niches and relied less on littoral carbon sources compared to littoral-caught conspecifics that included generalist as well as specialised benthivorous and planktivorous individuals. Despite the partially specialised planktivorous niche and thus reduced potential of pelagic-dwelling charr to promote benthic–pelagic coupling, the isotopic compositions of both charr subpopulations suggested a significant reliance on both littoral and pelagic carbon sources in all five study lakes.
6. Our study demonstrates that both interspecific niche segregation between and individual trophic specialisation within generalist fish species can constrain food-web coupling and alter energy mobilisation to top consumers in subarctic lakes. Nevertheless, pelagic and littoral habitats and food-web compartments may still be highly integrated due to the potentially plastic foraging behaviour of top consumers.