The Mamut Copper Mine (MCM) located in Sabah (Malaysia) on Borneo Island was the only Cu-Au mine that operated in the country. During its operation (1975During its operation ( -1999, the mine produced 2.47 Mt of concentrate containing approximately 600,000 t of Cu, 45 t of Au and 294 t of Ag, and generated about 250 Mt of overburden and waste rocks and over 150 Mt of tailings, which were deposited at the 397 ha Lohan tailings storage facility, 15.8 km from the mine and 980 m lower in altitude. The MCM site presents challenges for environmental rehabilitation due to the presence of large volumes of sulphidic minerals wastes, the very high rainfall and the large volume of polluted mine pit water. This indicates that rehabilitation and treatment is costly, as for example, exceedingly large quantities of lime are needed for neutralisation of the acidic mine pit discharge. The MCM site has several unusual geochemical features on account of the concomitant occurrence of acidforming sulphide porphyry rocks and alkaline serpentinite minerals, and unique biological features because of the very high plant diversity in its immediate surroundings. The site hence provides a valuable opportunity for researching natural acid neutralisation processes and mine rehabilitation in tropical areas. Today, the MCM site is surrounded by protected nature reserves (Kinabalu Park, a World Heritage Site, and Bukit Hampuan, a Class I Forest Reserve), and the environmental legacy prevents degazetting and inclusion in these protected area in the foreseeable future. This article presents a preliminary geochemical investigation of waste rocks, sediments, secondary precipitates, surface water chemistry and foliar elemental uptake in ferns, and discusses these results in light of their environmental significance for rehabilitation.