Seismic-volcanic unrest was detected between 2004 and 2005 in the central and northwest zones of Tenerife Island (Canary Islands, Spain). With the aim of strengthening the program of geochemical and seismic-volcanic surveillance, a study of the origin, characteristics, and spatial distribution of dissolved carbon dioxide (CO2) and helium (He) gases in the volcanic aquifer of central Tenerife Island and around Teide volcano was carried out. This work also improves the hydrogeological and hydrogeochemical conceptual model of groundwater flow. Dissolved CO2 concentrations in sampled groundwater are several orders of magnitude higher than that of air-saturated water (ASW) suggesting a significant contribution of non-atmospheric CO2, mainly magmatic, confirmed through measurement of isotopic compositions (δ13CTDIC) and total dissolved inorganic carbon (TDIC) concentrations. A vertical stratification of dissolved CO2 and δ13CTDIC values was observed in the volcanic aquifer at the eastern region of Las Cañadas Caldera. Stratification seems to be controlled by both degree of magmatic CO2-water interaction and CO2 degassing and the original δ13Cco2(g) isotopic composition. The highest dissolved helium (4He) concentrations in groundwater seem to be related to radiogenic contributions resulting from water-rock interactions, and increase with residence time, instead of with endogenous magmatic inputs. Isotopic systematics show that the dissolved gases in groundwater of central Tenerife are variable mixtures of CO2–3He-rich fluids of volcanic-hydrothermal origin with both organic and atmospheric components. The results suggest that the eastern area of Las Cañadas Caldera, the South Volcanic Ridge, and the Teide summit cone are the areas most affected by degassing of the volcanic-hydrothermal system, and they are therefore the most suitable zones for future geochemical monitoring.