Metabarcoding and metagenomic methods allowed us to analyze the diversity and structure of microbial communities in the sedimentary strata of Lake Baikal, in areas with quiet sedimentation and discharge of mineralized oil- and gas-bearing fluids. For all ecotopes (reference sites, mud volcanoes, and oil seeps), statistical analysis of metabarcoding data revealed a significant difference in the beta diversity between communities from oxidized and reduced layers of sediments (ANOSIM R = 0.79–0.80, pvalue < 0.001). A common feature of oxidized sediments was a higher relative abundance of Gammaproteobacteria, Desulfobacterota, Methylomirabilota, Verrucomicrobiota, Planctomycetota, and Nitrososphaeria. A large proportion of Atribacterota, Caldisericota, and Bathyarchaeia characterized the reduced sediments. Among ecotopes, communities differed mainly at the lower-ranked taxa level. Prokaryotes were more diverse in reduced sediments of discharge zones with high concentrations of methane of various origins and oil hydrocarbons. Special migration mechanisms and the chemical composition of fluids coming from deep layers of sedimentary strata provided the development of a wide range of bacteria and archaea that are phylogenetically different from their closest relatives (average nucleotide identity 74–79%). Genes for autotrophic carbon fixation (fdhAB, cooSF, acsBCD, porABCD, korABCD), sulfate reduction (asrABC, dsrAB, cysH), and methane generation/oxidation pathways (msrABCDG) prevailed in their genomes. Microbial communities from the oxidized sediment layers differed significantly in the prevalence of genes for carbon oxidation (glycolysis, oxidative phosphorylation), thiosulfate and sulfate oxidation (SOX, fccAB), as well as nitrification (amoAB, hao), denitrification (napAB, narGHI, nirKS, norBC, nosZ), and nitrite reduction (nirBD, nrfAH), whereas the relative proportion of the key genes for autotrophic CO2 fixation pathways was small. Compared to other freshwater lakes, metagenomes of microorganisms from Lake Baikal had a large proportion of nitrogen metabolism genes that ensured nitrification (amoAB, hao) and denitrification (nirKS, norBC, nosZ). This was also characteristic of metagenomes in the near-bottom area of the bathypelagic zone in Lake Baikal (Cabello-Yeves et al. Limnology and Oceanography, 65(7), 1471–1488, 2020). The diversity of abiotic conditions in Lake Baikal with the constant temperature regime over a rather long time (>25 million years) ensures the vital activity of cosmopolitan and endemic prokaryotes with unique genomic potential.