—Studies of helium isotope ratios in groundwaters discharging as springs within the Tunka–Oka–Sayan rift in the East Sayan area reveal an anomaly extending for 350 km along the East Sayan fault on the extension of the Tunka anomaly in the southwestern flank of the Baikal rift system. The calculated heat flow values (qR) agree with the measured ones (qT), and the heat flow anomalies correlate with those in the 3He/4He ratios throughout the Oka–Sayan and Bilin–Busiyn-Gol rifts. The correlation of the geophysical and geochemical parameters confirms that both are controlled by heat and mass transfer. Both mantle helium and heat apparently originate from a mantle plume beneath the South Baikal volcanic province (SBVP). The concordant 3He/4He and heat flow patterns in the Oka–Sayan fault record ongoing rifting and magmatism along the East Sayan Fault zone. The helium isotope and heat flow anomalies are consistent with the presence of low-velocity zones in the upper 200 km beneath the southwestern Baikal rift zone as far as the southern edge of the Siberian craton, which are detectable in seismic tomography images. Magmatism in the extreme southwest of the Baikal rift zone was maintained by active tectonic movements in the Pliocene and by the activity of the SBVP mantle plume. The obtained helium isotope data and high heat flow values indicate that rifting and magmatism propagate northwestward along the East Sayan Fault zone. This pattern fits the geothermal model for continental rifts implying that magmatic activity in the western end of BRS has been controlled by lithospheric deformation. The geothermal model for the Baikal–Mongolia region covers the area northwest of the system of three rift basins along the East Sayan faults.