Isotope-geochemical (δ2H and δ18O in H2O, δ15N in N2, δ13C in CO2 and CH4,3He/4He) studies of СО2-rich thermal waters (up to 41.3oC) which located in 4 km long tonnel of the Baksan Neutrino Observatory were carried out. The δ13C(CO2) values (–8.0… –6.4‰) indicate the volcanogenic genesis of CO2. The presence of the volcanogenic component is also emphasized by high values of 3He/4He (346 × 10–8). At the same time, nitrogen present in the gas phase is characterized by values of δ15N = +1.3‰, indicating its crustal genesis. In the tunnel, an elevated concentration of CH4 (up to 0.5%) was noted in one of the gas outlets. This methane is characterized by high δ13C values (–33.5 and –26.0‰), which, in general, are typical for other СО2-rich springs of the Eastern Elbrus Mountains. In contrast with the other CO2-rich springs of the North Caucasus, which are practically indistinguishable from surface waters in terms of δ2H and δ18O values, the CO2-rich thermal springs of the tunnel are noticeably enriched in heavy oxygen isotope (18O). This is a consequence of oxygen exchange between the waters and the host rocks at elevated temperatures. In the δ18O-δ2H diagram, the figurative points of thermal waters form a trend that reflects the mixing of isotope-light infiltration waters with isotope-heavy waters.