Across the globe, lake ecosystems are exposed to a variety of human disturbances. A notable example is shallow lakes where human-induced eutrophication or water level fluctuation may result in a switch from a clear-water, macrophyte-dominated state to a turbid, phytoplankton-dominated state. Yet, few investigations have described synchronous changes in biotic assemblage composition and food web framework under such a shift between alternative states. We used stable carbon and nitrogen isotopes to test the extent to which switching from macrophyte to phytoplankton dominance in Lake Gucheng, triggered by a water level increase, would alter ecosystem structure and change the basal resources supporting the food web. We found that invertebrates and fish compensated for a reduction of macrophyte and epiphyte resources by deriving more energy from the alternative pelagic energy channel, where benthic invertebrates act as crucial links between primary producers and higher consumers by transporting δ¹³C-depleted pelagic algae to the benthic zone. Although consumers can respond to large shifts in energy allocation and stabilize food web dynamics through their ability to feed across multiple energy pathways, our study suggest that energy subsidies may promote trophic cascades and enhance the stability of the turbid regime.