Rivers support some of Earth’s richest biodiversity and provide essential ecosystem services to society, but only if they flow. In Europe, attempts to quantify river connectivity have been hampered by the absence of a harmonised barrier database. We assembled ~630,000 unique barrier records from 36 European countries and surveyed 2,715 km of 147 rivers to reveal a ~61% underestimation of barrier numbers. We estimate there are at least 1.2 million instream barriers (mean density = 0.74 barriers/km), 72% of which are low-head (<2m) structures, making Europe the world’s most fragmented river landscape. The highest barrier densities occur in the heavily modified rivers of Central Europe, and the lowest in the most remote, sparsely populated alpine areas. Barrier density was predicted by agricultural pressure, road density, extent of surface water, and elevation. Relatively unfragmented rivers are still found in the Balkans, Scandinavia, the Baltic states, and parts of southern Europe, but these require urgent protection from new dam developments. Our findings can inform the implementation of the EU Biodiversity Strategy, which aims to reconnect 25,000 km of Europe’s rivers by 2030, but achieving this will require a paradigm shift in river restoration that recognises the impacts caused by small barriers.