Supergene copper mineralization occurs at the Kuh Toto deposit, located 25 km to the west of Torud village in the Semnan Province, Iran. Mineralogical, fluid inclusion and stable isotopic (C and O) studies, as well as rare earth element (REE) geochemistry of whole rock and minerals are used to unravel the conditions under which the Cu ores formed. Malachite is the only copper ore mineral, and it is present as veinlets, coatings and small patches in Eocene volcanic rocks. Malachite is accompanied by minor calcite, manganese and iron oxides and oxyhydroxides, clay minerals, epidote, quartz and chrysocolla. Argillic and, to a lesser extent, propylitic hydrothermal alteration partially affected the basic volcanic host rocks. The chondrite-normalized REE patterns of malachite and calcite are similar to those of the volcanic host rocks. They are enriched in LREEs. The volcanic host rocks are enriched in Cu (187 ppm on average). Fluid inclusions hosted in calcite reveal that calcite precipitated from hydrothermal fluids at low temperatures (69–150°C) and low to moderate salinities (7.17–11.10 wt% NaCl equivalent). The oxygen isotopic geothermometry yielded an average temperature of 41°C for malachite formation. Geochemical and fluid inclusion evidence strongly support that mineral-forming elements, including Cu, originated from the associated volcanic rocks. Available data support the view that Cu was likely leached as mobile aqueous Cu2+ from the volcanic rocks by oxidizing surface waters. When Cu-enriched fluids entered the underlying groundwater environment, Cu was precipitated as malachite in fractures, via recombination with carbonate ions dissolved as CO2 in meteoric fluids.