Cultural eutrophication of lakes due to excess loading of nutrients is a global problem affecting the provisioning of freshwater ecosystem services. Lake water quality is often described by trophic state indicators such as water clarity or concentrations of nutrients, chlorophyll, and cyanobacteria toxins. While these indicators are widely assumed to covary, capturing the same basic aspects of water quality, they can be uncoupled by changes in lake food webs. Outbreak of the invasive predatory zooplankton, Bythotrephes longimanus, in Lakes Mendota and Monona, Wisconsin (U.S.A.) in 2009 led to a decline in the herbivore, Daphnia pulicaria, and in turn, water clarity. We use 20‐yr datasets for Lakes Mendota and Monona to evaluate interactions among nutrients, zooplankton, and phytoplankton that resulted in this trophic cascade. After invasion, diatoms increased in both lakes resulting in reduced water clarity, whereas cyanobacteria did not change in either lake. Multivariate time series analysis revealed that D. pulicaria grazing controlled edible diatoms in both lakes. Cyanobacteria biomass was positively associated with both D. pulicaria and summer nutrient concentrations. These results further clarify the limitations of top‐down control in eutrophic lakes: grazing by zooplankton can control edible phytoplankton taxa, but largely inedible cyanobacteria may be more limited by nutrient concentrations. Accordingly, despite declining clarity in Lake Mendota, the number of beach closures due to cyanobacteria blooms declined following Bythotrephes invasion. Our study reveals how these two indicators of water quality—water clarity and cyanobacteria blooms—can become uncoupled during a food web shift.