Streams are significant sources of CO2 to the atmosphere. Estimates of CO2 evasion fluxes (fCO2) from streams typically relate to the free flowing water but exclude geomorphological structures within the stream corridor. We found that gravel bars (GBs) are important sources of CO2 to the atmosphere, with on average more than twice as high fCO2 as those from the streamwater, affecting fCO2 at the level of entire headwater networks. Vertical temperature gradients resulting from the interplay between advective heat transfer and mixing with groundwater within GBs explained the observed variation in fCO2 from the GBs reasonably well. We propose that increased temperatures and their gradients within GBs exposed to solar radiation stimulate heterotrophic metabolism therein and facilitate the venting of CO2 from external sources (e.g. downwelling streamwater, groundwater) within GBs. Our study shows that GB fCO2 increased f CO2 from stream corridors by [median, (95% confidence interval)] 16.69%, (15.85–18.49%); 30.44%, (30.40–34.68%) and 2.92%, (2.90–3.0%), for 3rd, 4th and 5th order streams, respectively. These findings shed new light on regional estimates of fCO2 from streams, and are relevant given that streamwater thermal regimes change owing to global warming and human alteration of stream corridors.