Capture and geological storage of CO2 is emerging as an attractive means of economically abating anthropogenic CO2 emissions from point sources. However, for the technology to be widely deployed it is essential that a reliable means to assess a site for both storage performance and regulation compliance exists. Hence, the ability to identify the origin of any CO2 seepage measured at the near-surface and ground surface and determine if it originates from a deep storage site or a different source is critical. As an analogue for post-emplacement seepage, here we examine natural CO2 rich springs and groundwater wells in the vicinity of the St. Johns Dome CO2 reservoir located on the border of Mid-Arizona/New Mexico, USA. Extensive travertine deposits in the region document a long history of migration of CO2 rich fluids to the surface. The presence of CO2 rich fluids today are indicated by high levels of HCO3 – in surface spring and groundwater well waters. We document measurements of dissolved noble gases and carbon isotopes from these springs and wells. We show that a component of the He fingerprint measured in gaseous CO2 sampled in the deep reservoir, can be traced along a fault plane to occur in waters from both groundwater wells and the majority of springs emerging at the surface above the reservoir. Our results show for the first time that CO2 can be fingerprinted from source to surface using noble gases and illustrates that this technique could be used to identify dissolved CO2 migration from engineered storage sites.