A commonly-used method in ore exploration is hydrogen peroxide ammonium citrate (HA) extraction, which has not typically been used in waste rock characterization. In this study, the sulfide specificity and leaching of other minerals in HA extraction was evaluated and its performance was compared with the aqua regia (AR) extraction for preliminary assessment of harmful element mobility. Samples collected from several different mine sites in Finland were utilized. The waste rock sample S contents ranged from 0.3% to 5.3%, and sums of the AR extractable elements As, Cd, Co, Cu, Ni and Zn range from 120 to 8040 mg/kg. The drainage types ranged from acid high-metal to neutral low-metal, with pH’s of 3.3–7.7. Mineralogical changes that took place in the HA solution were investigated by the field emission scanning electron microscope (FE-SEM) equipped with an energy-dispersive X-ray spectroscopy analyzer (EDS) and X-ray diffraction (XRD) methods. Results of the study showed that the HA extraction appears to be a more specific method for sulfide decomposition compared with AR extraction. Sulfide minerals, especially base metal sulfides pentlandite, chalcopyrite and sphalerite, decomposed efficiently in HA extraction. However, the Fe-sulfides pyrrhotite and pyrite only decomposed incompletely. The study showed that the HA extraction results can be used in the preliminary prediction of element mobility. Based on the results, the elevated As, Cd, Co, Cu, Ni, S and Zn leachability in the HA extraction appears to predict elevated drainage concentrations. If the HA-extractable sum of As, Cd, Co, Cu, Ni and Zn is >750 mg/kg, there is an increased risk of high-metal (>1000 µg/L) drainage. Therefore, the HA extraction data, e.g., produced during ore exploration, can be utilized to preliminary screen the risks of sulfide related element mobilities from waste rock material.