Food webs are strongly size-structured so will be vulnerable to changes in environmental factors that affect large predators. However, mechanistic understanding of environmental controls of top predator size is poorly developed. We used streams to investigate how predator body size is altered by three fundamental climate change stressors: reductions in habitat size, increases in disturbance and warmer temperatures. Using new survey data from 74 streams, we showed that habitat size and disturbance were the most important stressors influencing predator body size. A synergistic interaction between that habitat size and disturbance due to flooding meant the sizes of predatory fishes peaked in large, benign habitats and their body size decreased as habitats became either smaller or harsher. These patterns were supported by experiments indicating that habitat-size reductions and increased flood disturbance decreased both the abundance and biomass of large predators. This research indicates that interacting climate change stressors can influence predator body size, resulting in smaller predators than would be predicted from examining an environmental factor in isolation. Thus, climate-induced changes to key interacting environmental factors are likely to have synergistic impacts on predator body size which, because of their influence on the strength of biological interactions, will have far-reaching effects on food-web responses to global environmental change.