The large manganese (Mn) deposit at Obrochishte (NE Bulgaria) is part of a cluster of similar Early Oligocene deposits located around present-day Black Sea. They collectively constitute the Earth’s second largest endowment of Mn, after the Kalahari Manganese Field in Africa. We have employed a battery of isotopic techniques (C, O, Fe, Sr, Nd, Pb) to help understand the genesis of this deposit. Carbon isotope data indicates that some sections of the Mn-ore layer have diagenetic MnCO3 mineralization, formed by reaction of Mn oxides with organic carbon (Corg), whereas other sections have MnCO3 precipitated directly from the seawater column. Oxygen isotopes show that the high-grade Mn mineralization had seawater as the fluid source, whereas some lower-grade sections had a mix of ground water and seawater as fluid sources. Sr and Nd isotope values of ore leachates also indicate that the Mn deposition occurred in normal Early Oligocene seawater. Nd and Pb isotope values suggest that the clastic host sediments were sourced from continental bedrock rather than younger arc volcanic rocks to the west. Iron isotope composition of the Mn ore implies deposition in a redox-stratified basin, similar to the modern Black Sea, with much of the Fe sequestered in deep, anoxic-euxinic water as sulfides. Similar to the modern Black Sea, most of the detrital Fe was transferred from shallow oxic sediments into deep, anoxic-euxinic water by an “iron shuttle” and remobilized Mn sequestered in the upper suboxic water layer. However, during the Oligocene, the “iron shuttle” operated intermittently due to the chemocline falling mostly below the shelf break, thereby limiting the efficiency of the shuttle mechanism. We propose a model for the Lower Oligocene strata in which intense weathering during the Eocene weathering phase produced a thick lateritic crust on the southern European continent. The drastic sea-level drop at the end of the Eocene initiated downcutting of streams through this weathered material, transferring Fe- and Mn-oxides to the redox-stratified Western Black Sea. Here, these oxides were partly or entirely dissolved in the suboxic (Mn-oxides partly, Fe-oxyhydroxides entirely dissolved) and anoxic-euxinic (Mn-oxides entirely dissolved, dissolved Fe2+ re-precipitated) water layers. Eventually, Fe was re-precipitated as sulfide in the deep anoxic-euxinic water, while Mn accumulated in the suboxic water layer. Transgression in the Early Oligocene brought this Mn-rich water onto the shallow shelf where it precipitated as Mn-oxide, then converted to Mn-carbonates during early diagenesis. Some Mn was also contributed by submarine groundwater discharge. Further transgression brought lower-oxygen water onto the shelf and Mn-carbonate precipitated directly from the water column. The findings from this work provide insights about the unique Oligocene geochemical event in the region that lead to the formation of the 2nd largest cluster of Mn deposits in the world.