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Continental subsurface ecosystems are composed of rocks formed over the entire period of the Earth’s geological history. Various magmatic, metamorphic, and sedimentary rock combinations formed the environments holding the records of the highest registered temperature, pressure, pH, and salinity. The inhabitants of these hostile biotopes are estimated to constitute >10% of our planet’s total biomass. In a limited set of sampling sources for their investigation, deep subsurface mineral water aquifers remain essentially unacknowledged. Within an interdisciplinary study, we have monitored the chemical composition, phylogenetic and metabolic diversity of microbial communities at six different aquifers of Yessentukskoye mineral water deposit (Pre-Caucasus region) over the 3-year period. Thermal carbonaceous mineral waters from the Upper Cretaceous aquifer revealed the composition close to that presumed for the Proterozoic ocean. 16S rRNA profiles of several microbial communities, sampled from this same aquifer, significantly changed down its depth but were stable for each site over the sampling period. Deep phylogenetic lineages of uncultured microorganisms, such as Archaea of Hadarchaeales phylum or Actinobacteria of novel classes and orders, were highly represented in these communities. Beta diversity calculations outlined a group of prokaryotic taxa peculiar for the deep aquifer and not occurring in the upper zone of active hydrodynamic water exchange. Metagenomics-based optimal growth temperature calculations indicated these taxa to be thermophiles. MAGs analysis indicated methanogenic or acetogenic autotrophs to be the most represented metabolic groups in Proterozoic-like thermal waters, with Fe(III)-reducers being the second abundant group. An Fe(III)-reducing actinobacterium of OPB41 lineage was isolated into a pure culture, as well as several methanogenic Archaea. The biodiversity we have traced in our survey could reflect the composition of early Earth’s biosphere, as it experienced low evolutionary pressure due to high stability of physico-chemical conditions in continental water-bearing rocks over the geological time scale.