Recent studies have emphasized the importance of bedrock in hydrologic processes occurring in headwater catchments. To understand water flow processes through variously weathered bedrock, we measured the saturated hydraulic conductivity, Ks, and water retention characteristics of weakly to highly weathered Tanakami granite and Rokko granite core samples. On the basis of these core-scale properties, along with the core shape and in situ Ks measurements, we defined two groups of bedrock: CM class (weakly weathered) and CL to DL class (moderately to highly weathered). The CM class bedrock cores had almost no effective porosity (i.e., the amount of porosity that effectively contributes to water flow) and therefore extremely small core-scale Ks, indicating that the matrix could be regarded as essentially impermeable. The in situ Ks was much larger than the core-scale values, however, and the core shape showed apparent fractures, suggesting that water did flow preferentially through the fractures. The volumetric water content of the CL– to DL–class bedrock water retention curves changed little in the dry range but changed gradually in the wet range, resulting in a moderate core-scale Ks of 10−5 to 10−3 cm s−1. The core-scale Ks values were well explained by the parameters characterizing the water retention curve. The similarity of the in situ Ks to the core-scale values, and the lack of fractures in the core shape, suggested that water flow could be characterized as matrix flow. The hydraulic properties of weathered granite at other sites followed the trends observed at our sites, implying wide applicability of the findings in this study to various types of weathered granite.