Highly fractured rocks at Grasberg Mining in PT Freeport Indonesia (PTFI) lead to fractured groundwater flow media. Hydraulic conductivity of fractured rock has more complexity than that of porous rocks media. In this study, hydraulic conductivity (K) has been estimated according to HC-System based on Rock Quality Designation (RQD), Lithology Permeability Index (LPI), Depth Index (DI) and Gouge Content Designation (GCD). Numerical model of HC-System at Grasberg Mining in general can be expressed by the equation K = 2 x 10-6 x HC0.5571. The RQD data can be grouped into three ranges, i.e. first group that dominates over 80 % of the RQD data with K ranging between 1.9x10-8 – 2.3x10-7 m/s, second group that is within 40 – 80% of the RQD data with K falling between 2x10-8 – 7.2x10-7 m/s, and third group that takes part less than 40 % of RQD data with K ranging between 2.1x10-8 – 1.9x10-6 m/s. Based on the lithology, the hydraulic conductivity of rocks can be assinged as follows: igneous rock with K ranging 6.8x10-8 – 1.9x10-7 m/s, and sedimentary rock with K ranging 2.2x10-8 – 1.9x10-6 m/s. HC-System demonstrates good interpretation of hydraulic conductivity by means of clustering method, which uses geological and geotechnical data for hydrogeological characterization.