The Dead Sea Transform (DST) fault system, where a lateral displacement between the African and Arabian plates occurs, is characterised by anomalous heat flux in the Israeli area close to the border with Syria and Jordan. The concentration of He and CO2, and isotopic composition of He and total dissolved inorganic carbon were studied in cold and thermal waters collected along the DST, in order to investigate the source of volatiles and their relationship with the tectonic framework of the DST. The waters with higher temperature (up to 57.2 °C) are characterised by higher amounts of CO2 and helium (up to 55.72 and 1.91 * 10-2 cc l-1, respectively). Helium isotopic data (R/Ra from 0.11 to 2.14) and 4He/20Ne ratios (0.41-106.86) show the presence of deep-deriving fluids consisting of a variable mixture of mantle and crust end-members, with the former reaching up to 35%. Carbon isotope signature of total dissolved carbon from hot waters falls within the range of magmatic values, suggesting the delivery of deep-seated CO2. The geographical distribution of helium isotopic data and isotopic carbon (CO2) values coupled with (CO2/3He ratios) indicate a larger contribution of mantle-derived fluids affecting the northern part of the investigated area, where the waters reach the highest temperature. These evidences suggest the occurrence of a favourable tectonic framework, including a Moho discontinuity up-rise and/or the presence of a deep fault system coupled with the recent magmatic activity recognised in the northern part of Israel.