The Baikal rift system faults, having developed in the recent rift formation period, are characterized by hydrothermal and seismic activity. Especially in the northeastern part, the level of fracturing affects the localization of thermal outlets and the distribution of earthquake swarms. The specific features of the hydrothermal outputs and seismicity interposition, depending on the fracture heterogeneity and water saturation of the lithosphere layers, have not been previously evaluated. The results of the statistical analysis of the hydrothermal data, presented herein, show that most of the springs are distributed in areas of increased fault density. Multiple less hot hydrotherms are associated with zones of maximum density in the inter-block space. The spatio-temporal analysis of seismicity showed that migrations of weak and moderate seismic activity propagate from earthquake swarms through these zones. Swarms initiate the deformation front by propagating in the quasiplastic layer of the upper mantle at a speed of tens of kilometers per year, which can increase the aqueous fluid pore pressure in the lower earth’s crust, facilitate the movement of the fluid upwards along the section, and cause a process of successive stress relaxation in zones of high fracturing and concentration of hydrothermal springs. Earthquake swarms occur in areas of about average fracture density, associated with deep faults framing consolidated blocks of the earth’s crust. The hydrotherms with high or average temperature, and with probable deep source chemical composition components are related with such zones.