The effective geological storage of fluid CO₂ in porous subsurface rock will require the ability to track, and identify the origin of, any CO₂ seepage measured at the near surface. In a study relevant to postemplacement seepage, we examine natural CO₂ springs around Green River on the Colorado Plateau, United States, in an attempt to determine the CO₂ origins. We use a combination of natural geochemical and isotopic tracers to fingerprint the origin of CO₂ and water erupting at the surface. Stable oxygen and hydrogen isotope data enable the estimation that 80–90% of the spring water is derived from shallow groundwater, with the remainder originating from a deep saline aquifer. Carbon dioxide and water volumes imply the ascent of CO₂ as a separate fluid or gas, not just in solution in the pore water. Stable carbon isotopes of CO₂ are unable to discriminate between possible sources. However, the CO₂ contains trace amounts of noble gas isotopes, which can be used to demonstrate that approximately 0–20% of CO₂ erupted at the surface originates from the mantle, with the remainder originating from the crust. Within the study area, diverse noble gas signatures at different springs are observed, implying that no homogeneous free-phase accumulation at shallow depths exists as has been previously proposed. Natural tracers are, in this case, capable of resolving CO₂ origins and migration pathways. From this study, we conclude that the errors and uncertainty in tracing anthropogenically stored CO₂ will be reduced dramatically if a baseline survey is conducted to unambiguously characterize aquifer water chemistry, CO₂, and noble gas content, before the addition of anthropogenic CO₂ to the subsurface.