Abstract River networks contribute disproportionately to the global carbon cycle. However, global estimates of carbon emissions from inland waters are based on perennial rivers, even though more than half of the world's river length is prone to drying. We quantified CO 2 and CH 4 emissions from flowing water and dry riverbeds across six European drying river networks (DRNs, 120 reaches) and three seasons and identified drivers of emissions using local and regional variables. Drivers of emissions from flowing water differed between perennial and non‐perennial reaches, both CO 2 and CH 4 emissions were controlled partly by the annual drying severity, reflecting a drying legacy effect. Upscaled CO 2 emissions for the six DRNs at the annual scale revealed that dry riverbeds contributed up to 77% of the annual emissions, calling for an urgent need to include non‐perennial rivers in global estimates of greenhouse gas emissions.