The analysis of the formation of waste waters in the storage areas of ore and rock dumps of molybdenum deposits is carried out. It was stated that dump waters formed on these areas are contaminated with copper, molybdenum and iron in concentrations that exceed their maximum allowed concentration. To improve the flow, the technology associated with the cleaning of these piles of readily soluble forms of metal-pollutants using heap leaching was developed. Research was caried out on leaching of copper and molybdenum oxide ores of Zhirekenski deposits depending on the density of irrigation, the concentration of sulfuric acid, the pause between irrigations and duration of the process. The findings were processed using the method of Box- Wilson. As a result, the regression equation was obtained using which optimum conditions of the process were determined. Based on the results of studies a technological scheme of purification of molybdenum oxide ore dumps was designed.