A three-dimensional (3-D) discrete fracture network (DFN) geo-descriptive model is developed for water conducting features (WCFs) in the sedimentary formations of Horonobe underground research laboratory (URL) in Japan. Fracturing and faulting system in/around the URL area, which is the main investigation area of the Horonobe URL project, is characterized by taking into account borehole geophysical logging data, regional geologic/structural data, and fracture/fault data (orientation, intensity, size) obtained from the surface-based investigations. Volumetric fracture intensity potential is estimated by the correlation and the multi-linear regression analysis of observed data, and is used as one of controls for 3-D DFN model. A regional scale 3-D geo-descriptive DFN model is constructed based on the analyzed fracturing system identified for the WCFs. The current 3-D geo-descriptive model could be utilized explicitly to derive performance assessment (PA) parameters for the hypothetical repository of the high-level radioactive wastes in Japan, and to assist optimization of the safe repository design.