Ecological heterogeneity and intraspecific variation can impact energy flow from the base of the food web to top predators. We evaluated the effect of intraspecific variation on estimates of lake trout (Salvelinus namaycush) consumption of stocked kokanee (lacustrine sockeye salmon, Oncorhynchus nerka) in a 390 ha oligotrophic lake with two distinct basins. Lake trout stomach content analyses, stable isotope niche space, and catch rates indicated high intraspecific variation in resource use across habitats and basins. Intraspecific variation and ecological heterogeneity were incorporated into two bioenergetics modeling approaches; one lake-wide model, and one partitioned model that accounted for differences in lake trout diet composition and population size across habitats. The ecologically partitioned model highlighted that lake trout consumption was primarily in the epilimnion of one basin, while the lake-wide, unpartitioned model performed similarly but failed to provide ecological context for where that consumption occurred. Incorporating ecological heterogeneity and intraspecific variation into bioenergetic models can more accurately represent top predators foraging patterns across habitats and inform management actions to mitigate impacts to stocked fish.