Secure storage of anthropogenic carbon dioxide (CO2) in geological reservoirs requires predicting gas–water–rock interactions over millennial timescales. Noble gases and carbon isotope measurements can be used to shed light on the nature of competing dissolution—precipitation processes over different timescales, from the fast dissolution of gaseous CO2 in groundwater to more sluggish reactions involving dissolution and precipitation of newly formed minerals in the reservoir. Here we study a compilation of gas analyses including noble gases and δ13C of CO2 from nine different natural CO2 reservoirs. Amongst these reservoirs, the Bravo Dome CO2 field (New Mexico, USA) shows distinct geochemical trends which are explained by degassing of noble gases from groundwater altering the composition of the gas phase. This groundwater degassing is synchronous with the dissolution of CO2 in groundwater. Progressive creation of alkalinity via CO2-promoted mineral dissolution is required to explain the observed positive correlation between CO2/3He and δ13C of the gas phase, a unique feature of Bravo Dome. The differences between Bravo Dome and other natural CO2 reservoirs are likely explained by the more recent filling of Bravo Dome, reflecting CO2–water–rock interactions over thousands of years rather than over millions of years in older reservoirs.