Soil carbonates are dominantly present in dryland Critical Zone (CZ) and their formation could lead to important long-term carbon sequestration in arid to semiarid soils if the Ca ions were derived from silicate weathering or other non-carbonate sources. In managed CZ systems such as agricultural areas converted from natural drylands, irrigation has profound effects on the dryland CZ inorganic carbon storage, especially by modifying dissolution and precipitation dynamics of soil carbonates via controls of irrigation intensity and water chemistry, soil properties, and hydrological flow paths. These processes could lead to transformation of inorganic carbon in soils and groundwater aquifers underneath drylands. One key knowledge gap in studying soil carbonates from managed dryland CZ systems is to detect the formation of soil carbonates under irrigated conditions and distinguish them effectively from soil carbonates formed under natural conditions.Here, we explore the potential of using U-series and strontium isotopes to investigate the formation timescales and conditions of soil carbonates in both natural and managed dryland CZ in Chihuahua Desert of American Southwest. We obtained new U-series and Sr isotope ratios from mature stage V natural soil carbonates in the Jornada Basin of southern New Mexico and compared to previously published U-series and Sr isotope results for younger Jornada soil carbonates as well as irrigation impacted soil carbonates from the Rio Grande floodplains in west Texas. Specifically, we applied the U-series dating method (238U-234U-230Th) to estimate the timescales of soil carbonate formation under both natural climatic conditions and impacts of modern agriculture irrigation. In addition, we showed that the initial (234U/238U) activity ratios recorded in these soil carbonates reflect the systematic changes of soil infiltration rates in both natural and managed dryland CZ. We also utilized Sr isotope ratios (87Sr/86Sr) in soil carbonates, dust, and irrigation water to trace the Ca sources in soil carbonates from natural and managed dryland CZ. Soil carbonates from both settings were characterized by slightly radiogenic 87Sr/86Sr ratios, consistent with their potential of long-term carbon storage in drylands.U-series and Sr isotope systematics characterize important differences in soil carbonates from natural and managed dryland CZ with respect to their Ca sources, timescales of carbonate formation and transformation, and availability of soil moisture. Soil carbonates formed, accumulated, and transformed in natural drylands with long time scales but under irrigated arid agricultural areas its formation is significantly modified by irrigation and other agriculture practices, with implications for long- and short-term inorganic carbon sequestration in both systems of drylands.