Farmers in highlands in South Korea pile up 20 to 30 cm of saprolites, mostly granite- or granite-gneiss-weathered materials, on surface of arable lands every three to five years to compensate eroded soil and sometimes to discontinue soil-borne diseases. Immediate increases of infiltration and percolation rates are expected with coarse textured saprolites while soil drainage becomes poorer in a long-term. In this study, we analyzed mineralogical characteristics and micro-morphology of plow pan to investigate processes making impermeable layers. Soil samples were collected from plow pan, usually located at approximately 20 cm soil depth and at the lower part of piled saprolites, in arable lands in Hoenggye 5-ri, Daekwanryeong-myeon, Gangwon-do (N37.7, E128.7) in which saprolites were added 2, 4, and 8 years ago; saprolites were transported from similar areas. The saturated hydraulic conductivity decreased over time. Based on soil thin section pedography, quartz and feldspar accounted for a majority of minerals. The size of feldspar decreased and macropores became filled with clay or silt particles over time, which implies that macropores were packed with particles weathered from feldspar. The X-ray diffraction (XRD) analysis indicated that intensity of feldspar decreased over time and the reverse was true for kaolinite and illite, indicating that feldspar and mica weathering induced formation of kaolinite and illite. Conclusively, deteriorated drainage by formation of impermeable layers in farms with piled saprolites was caused by accumulation of clay minerals such as kaolinite and illite in macropores; illite and kaolinite can be formed by weathering of mica and feldspar, respectively.