Manganese mineralization is bound to Paleogene (Oligocene; Rupelian) and Jurassic (Toarcian, Aalenian and Bathonian–Callovian) shales. Mineralization is represented by manganese carbonates (rhodochrosite, kutnohorite and Mn-calcite). Mn-oxyhydroxides (pyrolusite, manganite and rancieite) were formed later during supergene processes by oxidation of manganese carbonates. Paleogene and Jurassic black shales with abundant framboidal pyrite are enriched in organic matter. The average content of organic carbon is 1.04 wt. % in Paleogene shale and 1.11 wt. % in Jurassic shale. The Si/Al ratios of 3.09 in Paleogene shale and 4.04 in Jurassic shale are close to typical marine-sediments and hydrogeneous-detrital manganese accumulations. The distribution of the rare earth elements in the shale suggests continental source and formation in more reducing environment than the Jurassic manganese crusts. Cobalt, copper and nickel contents of mineralized shale are distinctly lower than in oxidic ores in the Jurassic manganese crusts of Western Carpathians. Isotopic composition of calcite in sediments shows positive values δ¹³C in most samples of Paleogene and Jurassic carbonates. Increased manganese content in Mn-carbonates is closely associated with distinctly negative values of δ¹³C down to –9.9 in Paleogene carbonates and down to –11.2 in Jurassic carbonates. The dominant negative δ¹³C composition suggests early-diagenetic origin of Mn-carbonates affected by organic carbon.