Climate change is shifting the timing of organismal life-history events such as hatching, growth, reproduction, and migration. Although consequential food-web mismatches can emerge if predators and prey shift at different rates, research on phenological shifts has traditionally focused on single trophic levels. Here, we analyzed >2000 long-term, monthly time series of phytoplankton, zooplankton, and fish abundance or biomass for three major U.S. estuaries (San Francisco, Chesapeake, and Massachusetts bays). Phenological shifts occurred in over a quarter (27%) of the combined series and shifting taxa overwhelmingly advanced phenology. However, many (~34%-68%) taxa did not track the changing environment, and trends often diverged between predators and their potential prey. Notably, in the San Francisco Bay most fishes showed a delayed timing of peak abundance while many zooplankton peaked earlier, illustrating the potential for climate-driven trophic mismatch. Our results suggest that even if signatures of global climate change differ locally, widespread phenological change has the potential to disrupt estuarine food webs.