Freshwater biodiversity and ecosystem services are under stress as climate change alters streamflow intermittence. Some historically perennial rivers are now drying in most years, while non-perennial streams that once flowed into summer are reduced to disconnected pools by spring. We present the first continental-scale quantification of future climate change impacts on streamflow intermittence, achieved for Europe at a high spatial resolution that captures headwater streams. A hybrid modeling approach combined physics-based and data-based modeling, whereby a random forest model, trained on historical data, uses predictor values representing the impact of the changing climate on high-resolution (500 m) streamflow. These predictors were derived from the output of the low-resolution (50 km) global hydrological model WaterGAP, which was driven by bias-adjusted outputs of five global climate models. The generated monthly time series of intermittence status for over 1.5 million reaches were used to calculate five ecologically relevant indicators of streamflow intermittence change. In Europe, the number of non-perennial reach-months is projected to increase in the future, for both high (SSP5-RCP8.5) and low (SSP1-RCP2.6) greenhouse gas emissions scenarios, in almost all climate zones and in particular in August and September. Under SSP5-RCP8.5, 4.8% of all reach-months will experience no-flow conditions in the 2080s, up from 3.5% in 1985-2014, while only a small increase to 3.8% is projected under SSP1-RCP2.6. With high emissions, 2.8% of the European reaches are projected to shift from being perennial to being non-perennial by the 2080s, even in areas with increased annual precipitation, and 0.7% from non-perennial to perennial.