Predators are increasingly recognized as key elements in food webs because of their ability to link the fluxes of nutrients and energy between spatially separated food chains. However, in the context of food web connectivity, predator populations have been mainly treated as homogeneous units, despite compelling evidence of individual specialization in resource use. It is conceivable that individuals of a predatory species use different resources associated with spatially separated food chains, thereby decoupling cross-habitat linkages. We tested whether intrapopulation differences in habitat use in the generalist freshwater predator Eurasian perch (Perca fluviatilis) led to long-term niche partitioning and affected the degree of ecological habitat coupling. We evaluated trophic niche variability at successively larger timescales by analyzing gut contents and stable isotopes (delta13C and delta15N) in liver and muscle, tissues that provide successively longer integration of trophic activity. We found that the use of distinct habitats in perch led to intrapopulation niche partitioning between pelagic and littoral subpopulations, consistent through the various timescales. Pelagic fish showed a narrower niche, lower individual specialization, and more stable trophic behavior than littoral fish, as could be expected from inhabiting a relatively less diverse environment. This result indicated that substantial niche reduction could occur in a generalist predator at the subpopulation level, consistent with the use of a habitat that provides fewer chances of individual specialization. We showed that intrapopulation niche partitioning limits the ability of individual predators to link spatially separated food chains. In addition, we suggest a quantitative, standardized approach based on stable isotopes to measure the degree of habitat coupling mediated by a top predator.