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Methane (CH₄) is a potent greenhouse gas and its concentrations have tripled in the atmosphere since the industrial revolution. There is evidence that global warming has increased CH₄ emissions from freshwater ecosystems 1,2, providing positive feedback to the global climate. Yet for rivers and streams, the controls and the magnitude of CH₄ emissions remain highly uncertain 3,4. Here we report a spatially explicit global estimate of CH₄ emissions from running waters, accounting for 27.9 (16.7–39.7) Tg CH₄ per year and roughly equal in magnitude to those of other freshwater systems 5,6. Riverine CH₄ emissions are not strongly temperature dependent, with low average activation energy (E_M = 0.14 eV) compared with that of lakes and wetlands (E_M = 0.96 eV) 1. By contrast, global patterns of emissions are characterized by large fluxes in high- and low-latitude settings as well as in human-dominated environments. These patterns are explained by edaphic and climate features that are linked to anoxia in and near fluvial habitats, including a high supply of organic matter and water saturation in hydrologically connected soils. Our results highlight the importance of land–water connections in regulating CH₄ supply to running waters, which is vulnerable not only to direct human modifications but also to several climate change responses on land.