Physical processes may affect ecosystem structure and function through the accumulation, transport, and dispersal of organic and inorganic materials, nutrients, and organisms; they structure physical habitat and can influence predator–prey interactions and trophic production. In the Laurentian Great Lakes, horizontal currents generally dominate, but little is known about the effects of vertical mixing on lake food webs. We developed a linked earth system model and used it to explore how vertical mixing affects the productivity of Lake Michigan (LM), the world’s fifth-largest lake, whose food web and fisheries have been adversely affected by invasive Dreissena mussels. We hypothesized that higher vertical mixing would result in higher food web biomass by making phosphorus more available to the lower food web, and that filtration by invasive mussels would counter the effects of mixing and decrease food web biomass. Using linked climate, hydrodynamics, and ecosystem models, we projected the response of LM’s food web to scenarios of different levels of vertical mixing, with and without invasive mussels. Biomass of most functional food web groups increased with increases in vertical mixing, with the greatest increases in phytoplankton and zooplankton. Increased biomass was due to the replenishment of nutrients into the euphotic zone, which enhanced growth and biomass of lower trophic levels through bottom-up effects. However, filtration by invasive mussels reduced the positive effects of mixing for most species. Future applications of the linked earth system framework will explore the effects of climate warming and nutrient reduction on fisheries production to inform fisheries managers.