The Lake Huron ecosystem is unique among the Laurentian Great Lakes (USA/Canada) in that its surface area encompasses 3 distinct basins. This ecosystem recently experienced significant ecological restructuring characterized by changes in primary production, species dominance and abundances, and top predator energy dynamics. However, much of the evidence for this restructuring has been largely derived from biomonitoring data obtained from long‐term sampling of the lake's Main Basin. We examined polychlorinated biphenyl (PCB) concentrations and the stable isotopes of carbon (δ13C) and nitrogen (δ15N) in rainbow smelt (Osmerus mordax), bloater (Coregonus hoyi), and round goby (Neogobius melanostomus) to determine spatial variability in these environmental markers as indicators of the ubiquity of trophic restructuring throughout Lake Huron. Stable isotopes indicated that North Channel fish occupied trophic positions between 0.5 and 1.0 lower relative to Main Basin and Georgian Bay conspecifics, respectively. Sum PCB concentrations for 41 congeners were highest for fish from the Main Basin (27.5 ± 3.0 ng g−1 wet wt) and Georgian Bay (26.3 ± 3.4 ng g−1 wet wt) relative to North Channel (13.6 ± 1.2 ng g−1 wet wt) fish. Discriminant functions analysis demonstrated basin‐specific PCB congener profiles with individual species also having distinct profiles dependent on their basin of collection. These bioaccumulation patterns among Lake Huron forage fish mirror those reported for lake trout in this lake and indicate that the degree of food‐web ecological restructuring in Lake Huron is not equivalent across the basins. Specifically, basin‐specific PCB congener profiles demonstrated that differences among Lake Huron secondary and top predator consumer species are likely dictated by cross‐basin differences in zooplankton community ecology and trophodynamics that can regulate the efficiencies of prey energy transfer and PCB congener bioaccumulation patterns in aquatic food webs. Environ Toxicol Chem 2020;39:1712–1723. © 2020 SETAC