Data on geophysical fields and petrophysical heterogeneity, parageneses and the thermodynamic conditions and age of their formation, and fluid inclusions were used for the genetic reconstruction of petrophysical zoning at the Blagodatnoe gold-sulfide deposit. Petrophysical associations of the preore and ore stages of the deposit formation are clearly reflected in anomalies of the magnetic and natural electric fields and the aureoles of radioactive elements. At the early preore stage (752 Ma), reduced solutions with high activity of K, enriched in U, Th, and, probably, Au, were supplied to intensely foliated tectonic zones. Their interaction with initial metasedimentary rocks gave rise to contiguous zones of quartz–muscovite and chlorite metasomatic rocks. Accompanying graphitization led to a high electrochemical activity of the metasomatic rocks, which generated anomalies of up to –300 mV in the natural electric field; the most intensely carbonized zones became enriched with U (up to 6.5 × 10–4%) and, probably, Au. The quartz–muscovite metasomatic rocks accumulated Th and K (up to 29 × 10–4% and 4%, respectively), whereas the chlorite metasomatic rocks accumulated rock-forming elements (particularly Fe), which led to the compaction of these rocks and the acceleration due to gravity in local positive anomalies. The nonmagnetic character of the fresh pre-ore metasomatic rocks suggests the predominantly pyritic composition of early sulfides. At the ore stage (698 Ma), the minerals were deposited from H2O–CO2–As–S solutions at 560 to 315 °C. The activity of these solutions caused a redistribution of radioactive elements and a high petrophysical differentiation of the ore-bearing structure. The amplitudes of the anomalies above this structure vary from 500 to 80 nT in the magnetic field and from –130 to + 10 mV in the natural electric field. It has been found that the hydrothermal fluid hardly affected the polarization properties of graphitized rocks at the maximum temperatures but caused an intense removal of U and the development of magnetic pyrrhotite after pyrite. The temperature decrease in the mineral-forming system was favorable for the formation of siderite. Carbonaceous schists which experienced carbonatization lost their electrochemical activity. The binding of carbon dioxide in the solid phase influenced the migration capability of trace elements and their zonal distribution. With this evolution of the solution, Th accumulated at the lower levels of the mineralized zone, whereas the upper levels of the deposit became enriched with U. Productive gold–arsenopyrite–pyrite–pyrrhotite paragenesis with anomalous magnetic susceptibility evolved at the ore stage. The late galena–sphalerite–chalcopyrite paragenesis (365 Ma) was of strictly local occurrence and reduced the magnetic susceptibility of ores.