Background Groundwater is typically over-saturated in CO2 with respect to atmospheric equilibrium. Irrigation with groundwater is a common agricultural practice in many countries, but little is known about the fate of dissolved inorganic carbon (DIC) in irrigation groundwater and its contribution to the CO2 emission inventory from land to the atmosphere. We performed a mesocosm experiment to study the fate of DIC entering agricultural drainage channels in the North China Plain. Specifically, we aimed to unravel the effect of flow velocity and nutrient on CO2 emissions. Results All treatments were emitting CO2. Approximately half of the DIC in the water was consumed by TOC production (1-16%), emitted to the atmosphere (14-20%), or precipitated as calcite (CaCO3) (14-20%). We found that DIC depletion was stimulated by nutrient addition, whereas more CO2 evasion occurred in the treatments without nutrients addition. On the other hand, about 50% of CO2 was emitted within the first 50h under high flow velocity. Thus, in the short term, high nutrient levels may counteract CO2 emissions from drainage channels, whereas the final fate of the produced biomass (burial versus mineralization to CO2 or even CH4) determines the duration of the effect. Conclusion Our study reveals that both hydrology and biological processes affect CO2 emissions from groundwater irrigation channels. The estimated CO2 emission from total groundwater depletion in the North China Plain is up to 0.52 ± 0.07 Mt CO2 y−1. Thus, CO2 emissions from groundwater irrigation should be considered in regional CO2 budgets, especially given that groundwater depletion is expected to acceleration in the future.