In many food webs, species in similar trophic positions can interact either by competing for resources or boosting shared predators (apparent competition), but little is known about how the relative strengths of these interactions vary across environmental gradients. Introduced Mysis diluviana shrimp interact with planktivorous fishes such as kokanee salmon (lacustrine Oncorhynchus nerka) through both of these pathways, and effective management depends on understanding which interaction is more limiting under different conditions. An “environmental matching” hypothesis predicts the ecological impacts of Mysis are maximized under cool conditions near its thermal optimum. In addition, we hypothesized Mysis is more vulnerable to predation by lake trout in relatively shallow waters, and therefore Mysis enhances lake trout density and limits kokanee through apparent competition more strongly in shallower habitats. We tested whether these hypotheses could explain food web differences between two connected lake basins, one relatively shallow and the other extremely deep. The shallower basin warmed faster, thermally excluded Mysis from surface waters for 75% longer, and supported 2.5–18 times greater seasonal production of cladoceran zooplankton than the deeper basin, standardized by surface area. Mysis consumed 14–22% less zooplankton in the shallower basin, and lower ratios of total planktivore consumption to zooplankton production (C:P) indicated less potential for resource competition with kokanee, consistent with environmental matching. Lake trout diets contained more Mysis in the shallower basin and at shallower sampling sites within both basins. The catch rate of lake trout was seven times greater and the predation risk for kokanee was 4–5 times greater in the shallower basin than in the deeper basin, consistent with stronger apparent competition in shallower habitats. Understanding how the strengths of these interactions are mediated by temperature and depth would enable managers to select appropriate strategies to address the unique combinations of conditions in hundreds of affected systems.