Irrigated agriculture is conducted on approximately 257 million hectares worldwide and continues to expand, particularly in arid to semi-arid regions. Applications of water containing dissolved calcium and bicarbonate ions cause the precipitation of calcium carbonate in the soil and the release of carbon dioxide into the air. However, the contribution of inorganic C to CO2 emissions from the soil is rarely considered. Using a short-term incubation technique developed to examine changes in mineralizable organic C pools, we found that soils beneath drip emitters in an irrigated apple orchard released CO2 from both organic and inorganic C. Soils under drippers had higher concentrations of carbonates than soils that had not received direct inputs of irrigation water. The quantity of carbonates detected in the soil under the drippers at this site was small but may be greater on sites using irrigation water with higher concentrations of Ca2+ and HCO3-. Furthermore, site productivity may be reduced by unfavourable physical and chemical changes caused by carbonate deposition within the small soil volume occupied by tree roots in micro-irrigated orchards with dwarfing rootstocks. In order to better understand the implications for site productivity and for global C flux of carbonate precipitation in micro-irrigated systems, future work is required to quantify CO2 emissions during irrigation, and to characterize soil chemical and physical properties through the soil profile.