The Mowana hydrothermal Cu deposit is located within the Matsitama–Motloutse Complex in the southwestern part of the Zimbabwe Craton in the northeastern part of Botswana. This study aims to document the characteristics of the mineralization based on geology, quartz textures, ore mineralogy, chlorite geothermometry, and sulfur isotope analyses. The deposit is hosted by the NNE‐striking and nearly vertically dipping (70–80°) Bushman Lineament, within the graphitic schist lenses in the carbonaceous and argillaceous metasedimentary rocks of the Neoarchean to Paleoproterozoic Matsitama Sedimentary Group. The hydrothermal alteration of the host rocks is characterized by silicification, chloritization, epidotization, sericitization, hematite, and calcite alteration. Based on the alteration mineral assemblage, the main mineralization stage is attributed to near neutral pH fluids at temperatures between ~200 and ~340°C. The base metal mineralization of the Mowana deposit was evolved in at least two vein types. The first mineralization type, represented by the quartz+calcite±K‐feldspar veins and breccias is characterized by the precipitation of principal chalcopyrite with pyrite, minor bornite, and trace amounts of galena. The Type 2 veins represented by the quartz+calcite±fluorite veins, host appreciable amounts of galena. The supergene mineralization widely distributed in the shallow levels of the deposit is manifested by the significant presence of chalcocite, bornite, covellite, anglesite, malachite, and hematite. The temperature obtained from the chlorite geothermometry in the Type 1 veins indicate that the mineralization associated with chlorite alteration formed at a temperature ranging from 340 to 400°C. The ore mineral assemblage: pyrite, bornite, and chalcopyrite, paired with the chlorite geothermometry data indicate that the Type 1 veins formed at an intemediate to high sulfidation state. Sulfur isotopic ratios determined on the sulfides indicate the magmatic S and/or leaching of the host metasedimentary rocks and closed system reduction of seawater sulfate as the sources of S.