The Parnok deposit is made up of stratiform lodes of iron (magnetite) and manganese (oxide-carbonate, carbonate, and carbonate-silicate) ores localized among terrigenous-carbonate sediments (black shales) on the western slope of the Polar Urals. The lithological study showed that ore-bearing sediments were accumulated in a calm hydrodynamic setting within a relatively closed seafloor area (trap depressions). Periodic development of anaerobic conditions in the near-bottom seawater was favorable for the accumulation of dispersed organic matter in the terrigenous-carbonate sediments. Carbon required to form calcium carbonates in the ore-bearing sediments was derived from carbon dioxide dissolved in seawater. In the organic-rich sediments, carbonates were formed with the participation of carbon dioxide released by the destruction of organic matter. However, δ13C values (from 0.5 to −4.4‰ PDB) suggest a relatively low fraction of the isotopically light biogenic carbon in the host calcite. The most probable sources of Fe and Mn were hydrothermal seepages at the seafloor. The Eh-pH conditions during stagnation were favorable for the precipitation of Fe and accumulation of Mn in a dissolved state. Transition from the stagnation regime to the concentration of oxygen in near-bottom waters was accompanied by oxidation of the dissolved Mn and its precipitation. Thus, fluctuations in Eh-pH parameters of water led to the differentiation of Fe and Mn. Initially, these elements were likely precipitated as oxides and hydroxides. During the subsequent lithification, Fe and Mn were reduced to form magnetite and rhodochrosite. The texture and structure of rhodochrosite aggregates indicate that manganese carbonates already began to form at the diagenetic stage and were recrystallized during the subsequent lithogenetic stages. Isotope data (δ13C from −8.9 to −17.1‰ PDB) definitely indicate that the oxidized organic matter of sediment served as the main source of carbon dioxide required to form manganese carbonates. Carbonates from host rocks and manganese ores have principally different carbon isotopic compositions. Unlike carbonates of host rocks, manganese carbonates were formed with an active participation of biogeochemical processes. Further processes of metagenesis (T ≈ 250–300°C, P ≈ 2 kbar) resulted in the transformation of textures, structures, and mineral composition of all rocks of the deposit. In particular, increase in temperature and pressure provided the formation of numerous silicates in manganese ores.