The Cape Vani Mn oxide and barite deposit on Milos Island offers an excellent opportunity to study the three-dimensional characteristics of a shallow-water hydrothermal system. Milos Island is part of the active Aegean volcanic arc. A 1 km long basin located between two dacitic domes in northwest Milos is filled with a 35-50 m thick section of Quaternary volcaniclastic and pyroclastic rocks capped by reef limestone that were hydrothermally mineralized by Mn oxides and barite. Manganese occurs as thin layers, as cement of sandstone and as metasomatic replacement of the limestone, including abundant fossil shells. Manganese minerals include chiefly δ-MnO2, pyrolusite and ramsdellite. The MnO contents for single beds range up to 60%. The Mn oxide deposits are rich in Pb (to 3.4%), BaO (to 3.1%), Zn (to 0.8%), As (to 0.3%), Sb (to 0.2%) and Ag (to 10 ppm). Strontium isotopic compositions of the Mn oxide deposits and sulphur isotopic compositions of the associated barite show that the mineralizing fluids were predominantly sea water. The Mn oxide deposit formed in close geographical proximity to sulphide-sulphate-Au-Ag deposits and the two deposit types probably formed from the same hydrothermal system. Precipitation of Mn oxide took place at shallow burial depths and was promoted by the mixing of modified sea water (hydrothermal fluid) from which the sulphides precipitated at depth and sea water that penetrated along faults and fractures in the Cape Vani volcaniclastic and tuff deposits. The hydrothermal fluid was formed from predominantly sea water that was enriched in metals leached from the basement and overlying volcanogenic rocks. The hydrothermal fluids were driven by convection sustained by heat from cooling magma chambers. Barite was deposited throughout the time of Mn oxide mineralization, which occurred in at least two episodes. Manganese mineralization occurred by both focused and diffuse flow, the fluids mineralizing the beds of greatest porosity and filling dilatational fractures along with barite.