Turnover in species composition through time is a dominant form of biodiversity change, which has profound effects on the functioning of ecological communities1,2,3,4. Turnover rates differ markedly among communities4, but the drivers of this variation across taxa and realms remain unknown. Here we analyse 42,255 time series of species composition from marine, terrestrial and freshwater assemblages, and show that temporal rates of turnover were consistently faster in locations that experienced faster temperature change, including both warming and cooling. In addition, assemblages with limited access to microclimate refugia or that faced stronger human impacts on land were especially responsive to temperature change, with up to 48% of species replaced per decade. These results reveal a widespread signal of vulnerability to continuing climate change and highlight which ecological communities are most sensitive, raising concerns about ecosystem integrity as climate change and other human impacts accelerate.