Waste-rock dumps and water quality of pit-lakes formed at abandoned mines of pyrite-rich ore deposits are of considerable environmental concern around the world. The Mathiatis and Sha mines provide typical examples of abandoned mines where Cyprus-type Cu-pyrite ore was exploited. Supergene alteration of the sulphide ore and the mine waste leads to the formation of efflorescence and generation of acid mine drainage (AMD) filling the pit-lakes. Sulphate concentrations range from 4,600 to 4,850 mg/L and from 35,900 to 38,500 mg/L for the Mathiatis and Sha mines, respectively. Concentrations of heavy metals exceed the established regulatory limits in water. A preliminary assessment of the mine waste at the Mathiatis mine indicated that it cannot be characterized as inert material according to European legislation, posing an environmental threat as a source of AMD. The identified Mg, Ca and Fe efflorescence mineral phases retain temporarily trace metals near the mine waste and the pit-lake shore. Neutralisation experiments on the acidic waters of the epilimnion indicated local limestone is not sufficient for full remediation. However, it could be used as a low-cost pretreatment method for AMD. The study expands the international database of AMD affected areas and provides the basis for future remediation efforts.