Carbon dioxide (CO2 ) fluxes in the vadose zone are influenced by a complex interplay of biological, chemical and physical factors. A soil mesocosm system was designed to assess the effect of agricultural practices on carbon fluxes within and out of the 5 vadose zone at controlled environmental conditions. Carbon dioxide partial pressure (pCO2 ), alkalinity, soil moisture and temperature were measured with depth and time, and DIC in the percolate was quantified using a sodium hydroxide trap. Results showed good reproducibility between two replicate mesocosms. The pCO2 varied between 0.2– 1.1 % and alkalinity was 0.1–0.6 meq L−1 . The measured effluent DIC flux was 185– 196 mg L−1 m −2 10 and in the same range as estimates derived from pCO2 and alkalinity in samples extracted from the side of the mesocosm column, and the water flux. The relatively small variation provides confidence that the mesocosm system is a promising tool for studying a range of processes in unsaturated environments. Meanwhile, high suction at the mesocosm bottom applied to reduce water ponding during intensive irrigation caused degassing of dissolved CO2 15 from the water phase just below the outlet, leading to diffusion of dissolved CO2 across the lower boundary. Though not influencing DIC flux measurements to the groundwater, this lead to a lowering of the pCO2 in the stagnant water at the mesocosm bottom. A free-drainage boundary is suggested in order to avoid this effect