In this study, we make a quantitative assessment on the volatile flux of mantle-derived fluids and source of volatiles to explain the geologic controls on the transport of volatiles within thermal fluids of northeastern Anatolia. In line with this objective, we collected 22 samples (gas and water phase) from 16 geothermal fields in NE Turkey covering an area of nearly 100,000 km2 that extends from the eastern termination of North Anatolian Fault towards the Georgian and Armenian borders. The 3He/4He ratios of the samples (R) normalized to the atmospheric 3He/4He ratio (Ra = 1.4 × 10−6) vary from 0.31 to 7.15, and are considerably higher than the crustal value of 0.02Ra. Regarding spatial distribution of helium isotope composition, samples collected from areas of tectonic unrest around the Erzincan and Erzurum pull-apart basins in the southern part are represented by a higher range of 3He/4He ratios (>5 Ra) than those in volcanic areas to the east and northeast of the region. δ13CCO2 values of the gas samples varying from −20.76 to 5.43 ‰ are about 4–5 ‰ lower than δ13CDIC values of the water samples that range from −16.90 to 8.85 ‰, indicating CO2 removal from waters by degassing. CO2/3He ratios of gas samples falling in the range of 3.81 × 109 to 2.83 × 1012 imply that carbon is derived from the mixing between the crustal lithologies and mantle, the latter having a contribution up to 40 %. The maximum flux of mantle-derived fluids is found 88 mm/a at Erzincan (eastern part of the North Anatolian Fault Zone). This value is higher by a factor of about 10 than the western part of the fault zone. Calculations show that degassing from magmatic bodies is the sole mechanism to explain the high helium isotope compositions in the region. Therefore, we suggest that mantle-derived He contents might be due to extensive melting associated with active tectonism. The 3He/Heat ratios of thermal waters in northeastern Turkey were calculated in range of 0.25 to 29.7 × 10−15 cm3(STP)/J, consistent with the data reported for waters along the North Anatolian Fault, indicating a crustal heat source for the geothermal systems in northeastern Turkey.