Dryland ecosystems are experiencing more variability and extremes in rainfall and disproportionate shifts in plant community composition, both likely to alter soil carbon (C) cycling and storage. Although most studies focus on changes in soil organic C (SOC) pools, inorganic C (SIC) pools in drylands are susceptible to disturbances and may represent an important sink. We report changes in soil organic carbon (SOC) and inorganic carbon (SIC) isotopic values in the top 1 m of soil profiles following ~20 years of experimental manipulation of water availability and vegetation within a cold-desert ecosystem. The changes in C isotopic values correspond to reported changes in SOC and SIC pools relative to ambient controls. We used a split plot design (n = 3) contrasting vegetation types (split plot), either native Artemisia tridentata spp. tridentata (big sagebrush) communities or monocultures of Agropyron cristatum (crested wheatgrass), a non-native bunchgrass, in manipulations of spring/fall (DORM) or summer (GROW) water availability (whole-plot) all stratified by under-plant vs. inter-plant patch microsite. Despite increases in pedogenic SIC pools in inter-plant patches, under crested wheatgrass in DORM treatments, and under sagebrush in GROW treatments, we detected little corresponding change in SIC-δ13C or δ18O values. Average SIC-δ13C or δ18O values were -4.12 and -13.10‰, respectively, and suggest a mixture of atmospheric and respired carbon dioxide (CO2) sources and groundwater HCO3-. Both SIC and SOC-δ13C values were more depleted in GROW treatments (∆13C = -0.10 and -0.5‰ respectively), while SIC-δ18O values were more enriched (∆18O = 0.02‰). SIC-δ13C profiles became more enriched in surface horizons and deleted at depth relative to ambient. SIC- δ18O values were enriched in surface horizons under crested wheatgrass but not sagebrush. We conclude that both change in the timing and availability of water, and vegetation can change SIC storage and potentially the relative mixture of C sources. However, suitable methods for assessing SIC-C sources with changing storage in native soils are lacking and limit our understanding of SIC in the changing global C budget. Further methodological development is required along with long-term experimental manipulations geared for testing the role of SIC in C sequestration on human timescales.