Zebra mussels (Dreissena polymorpha), an aquatic invasive species, shift lake food resources from the pelagic to the littoral zone, while simultaneously altering physical habitat by increasing water clarity. Using stable isotope analysis, we find that walleye (Sander vitreus), a specialist piscivore with strict habitat requirements, and yellow perch (Perca flavescens), a generalist in both diet and habitat, respond similarly to food web and habitat differences in zebra mussel invaded lakes, with significant increases in littoral reliance from ~50% to ~75% for both species. We also report a correlated increase in mercury concentrations in fish tissue, which were 66% higher for adult walleye and 90% higher for adult yellow perch in lakes containing zebra mussels. Considering the importance of these fish for consumption, it is critical that we understand how changes to nutrient cycling and lake food webs ultimately increase toxin concentration in fish consumed by humans.