Invasive fish alter ecosystems and can reduce native species inducing a trophic cascade. Several methods are used to control or eradicate invasive fish; however, the success of methods vary among ecosystems and few programs monitor outcomes. Plankton can be used to evaluate the effectiveness of control measures because they have short lifespans and are sensitive to changes in food webs. We monitored plankton in Yellowstone Lake, and we compared phytoplankton and zooplankton assemblages to data collected pre- and post-lake trout (Salvelinus namaycush) invasion to assess how control measures altered the food web. Efforts to control lake trout increased by 10-fold in 2012 resulting in 300,000 fish being removed annually. Phytoplankton biomass decreased, and the biomass and individual size of large zooplankton increased following the invasion of piscivorous lake trout and concurrent decline of native, planktivorous cutthroat trout (Oncorhynchus clarkii bouvieri). Phytoplankton biomass, measured as chlorophyll a, and Secchi disk depth did not change when more Lake Trout were removed. The zooplankton assemblage continues to be dominated by large species with longer individual body lengths after efforts increased. The length of Hesperodiaptomus shoshone, a large copepod, decreased due to juvenile lake trout targeting this prey. The plankton assemblage indicated that Yellowstone Lake continues to be dominated by lake trout despite a large effort to control the adult stage of these fish with gill nets; however, some metrics are changing toward the historical configuration. Historical data are critical to use as benchmarks in conservation efforts to restore the native food web configuration.