<p>Invasive species disrupt food webs, and understanding the trophic structure of communities before invasion is fundamental to determining how invaders may harm native species and ecosystems. Because environmental factors shape food web dynamics, different systems are likely to respond differently to the same invader. Lake Champlain has five discrete basins with distinct trophic states and morphometries but similar species and thus provides a unique opportunity to investigate the potential for varied responses to invaders in lake systems. We evaluated (i) the relative importance of benthic and planktonic producers to the nearshore and offshore food webs of each lake basin, (ii) compared trophic positions among fish species, and (iii) estimated fish isotopic niches to evaluate variations in nearshore and offshore communities. Our results indicated that in the eutrophic shallow basins, benthic-derived carbon supported the food web. In mesotrophic, moderate-deep basins, pelagic and benthic resources equally contributed to supporting the food web, and coolwater piscivores couple nearshore and offshore habitats. In the deepest basin, two distinct food webs were clear with almost no interaction between offshore and nearshore species. Given our results, we expect a likely incipient quagga mussel (<i>Dreissena bugensis</i>) invasion will reduce planktonic carbon available for forage fishes in the deepest basins and negatively impact nearshore and offshore food webs, with higher impacts on the latter. Round goby (<i>Neogobius melanostomus</i>) invasion will likely result in competition with native fishes for space and food resources in nearshore habitats and thus alter trophic pathways in littoral food webs in all basins.</p>