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Agricultural fields in drylands are challenged globally by limited freshwater resources for irrigation and also by elevated soil salinity and sodicity. It is well known that pedogenic carbonate is less soluble than evaporate salts and commonly forms in natural drylands. However, few studies have evaluated how irrigation loads dissolved calcium and bicarbonate to agricultural fields, accelerating formation rates of secondary calcite and simultaneously releasing abiotic CO₂to the atmosphere. This study reports one of the first geochemical and isotopic studies of such “anthropogenic” pedogenic carbonates and CO₂from irrigated drylands of southwestern United States. A pecan orchard and an alfalfa field, where flood-irrigation using the Rio Grande river is a common practice, were compared to a nearby natural dryland site. Strontium and carbon isotope ratios show that bulk pedogenic carbonates in irrigated soils at the pecan orchard primarily formed due to flood-irrigation, and that approximately 20–50% of soil CO₂in these irrigated soils is calcite-derived abiotic CO₂instead of soil-respired or atmospheric origins. Multiple variables that control the salt buildup in this region are identified and impact the crop production and soil sustainability regionally and globally. Irrigation intensity and water chemistry (irrigation water quantity and quality) dictate salt loading, and soil texture governs water infiltration and salt leaching. In the study area, agricultural soils have accumulated up to 10 wt% of calcite after just about 100 years of cultivation. These rates will likely increase in the future due to the combined effects of climate variability (reduced rainfall and more intense evaporation), use of more brackish groundwater for irrigation, and reduced porosity in soils. The enhanced accumulation rates of pedogenic carbonate are accompanied by release of large amounts of abiotic CO₂from irrigated drylands to atmosphere. Extensive field studies and modelling approaches are needed to further quantify these effluxes at local, regional and global scales.