CO₂ outgassing from small streams causes one of the main uncertainties in global carbon budgets. These are caused by variable flow conditions, changing stream surface areas, and groundwater seeps. Here we used groundwater data to improve a novel stable carbon isotope modelling approach. We found that CO₂ outgassing contributed more than three-fourths of annual stream inorganic carbon loss in a small, silicate catchment. We underline the potential of this approach for global applications.