—A model of deep electrical conductivity of the Altai–Sayan folded region is presented, which was compiled from the results of three-dimensional inversion of the invariant values of the impedance matrix and interactive selection of three-dimensional model curves of magnetotelluric sounding to experimental ones. The obtained electrical resistivity values were used to estimate the fluid saturation of the Earth’s crust by applying the Shankland–Waff equation. The NaCl salinity of the aqueous solution is taken equal to 170 g/L, for which the fluid saturation is most consistent with the seismic data. The electrical conductivity and fluid saturation of focal zones of earthquakes, activated blocks of the region and deep faults were studied. Most of the earthquake hypocenters are located above the top of the conductors and near deep low-resistivity faults. The position of low-resistivity anomalies correlates with the position of domains with the enhanced attenuation of converted earthquake waves and reduced velocities of compressional waves. The Teelin, Samagaltai, and Kaa-Khem earthquake sources are characterized by the maximum fluid content (0.5–0.9%), and the Altai, Shapshal, Shagonar and Bolsheporoshskii sources, by minimum ones (0.1–0.2%). The fluid saturation of deep faults reaches 1.2%. The faults characterized by tensile stresses oriented orthogonally to their strike, show the highest fluid content. A similar pattern is observed for the crustal blocks located beneath depressions. The high fluid content beneath the Kyzyl Basin and its surroundings correlate with the major compressional-wave velocity deficit beneath it.