AbstractSoil carbonates (i.e., soil inorganic carbon or SIC) represent more than a quarter of the terrestrial carbon pool and are often considered to be relatively stable, with fluxes significant only on geologic timescales. However, given the importance of climatic water balance on SIC accumulation, we tested the hypothesis that increased soil water storage and transport resulting from cultivation may enhance dissolution of SIC, altering their local stock at decadal timescales. We compared SIC storage to 7.3 m depth in eight sites, each having paired plots of native vegetation and rain‐fed croplands, and half the sites having additional irrigated cropland plots. Rain‐fed and irrigated croplands had 328 and 730 Mg C/ha less SIC storage, respectively, compared to their native vegetation (grassland or woodland) pairs, and irrigated croplands had 402 Mg C/ha less than their rain‐fed pairs (p < .0001). SIC contents were negatively correlated with estimated groundwater recharge, suggesting that dissolution and leaching may be responsible for SIC losses observed. Under croplands, the remaining SIC had more modern radiocarbon and a δ13C composition that was closer to crop inputs than under native vegetation, suggesting that cultivation has led to faster turnover and incorporation of recent crop carbon into the SIC pool (p < .0001). The losses occurred just 30–100 years after land‐use changes, indicating SIC stocks that were stable for millennia can rapidly adjust to increased soil water flows. Large SIC losses (194–242 Mg C/ha) also occurred below 4.9 m deep under irrigated croplands, with SIC losses lagging behind the downward‐advancing wetting front by ~30 years, suggesting that even deep SIC were affected. These observations suggest that the vertical distribution of SIC in dry ecosystems is dynamic on decadal timescales, highlighting its potential role as a carbon sink or source to be examined in the context of land use and climate change.