There are the results of a study of the factors determining the formation and changes in the filtration properties of a heap leaching stack formed from pelletized poor sandy-clay ores. An analysis of methods of investigation of filtration properties of ore material for different stages of heap leaching plots functioning is carried out. Influence of segregation process during stack dumping on formation of zones with very different permeability parameters of ore has been established by experimental and filtration works. The construction and application of a numerical model of filtration processes in pelletized ores based on laboratory experiments is shown. By means of solution percolation simulation at different irrigation intensities the justification of optimal stack parameters is provided in terms of the geomechanical stability and prevention of solution level rise above the drainage layer.