Rivers support some of Earth’s richest biodiversity1 43 and provide essential ecosystem services to society but they are often impacted by barriers to freeflow. In Europe, attempts to quantify river connectivity have been hampered by the absence of a harmonised barrier database. Here we show that there are at least 1.2 million instream barriers in 36 European countries (mean density = 0.74 barriers/km), 68% of which are low-head (<2 m) structures that are typically unreported. Standardised walkover surveys along 2,715 km of stream length in 147 rivers indicate that existing records underestimate barrier numbers by ~61%. The highest barrier densities occur in the heavily modified rivers of Central Europe, and the lowest in the most remote, sparsely populated alpine areas. Across Europe, the main predictors of barrier density are agricultural pressure, density of river-road crossings, extent of surface water, and elevation. Relatively unfragmented rivers are still found in the Balkans, the Baltic states, and parts of Scandinavia and 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 widespread impacts caused by small barriers.