Recent studies have suggested that bedrock groundwater can exert considerable influence on runoff generation, water chemistry, and the occurrence of landslides in headwater catchments. To clarify water infiltration and redistribution processes between soil and shallow bedrock and their effect on storm and base flow discharge processes in a small headwater catchment underlain by weathered granite, we conducted hydrometric observations using soil and bedrock tensiometers combined with hydrochemical measurements and water budget analyses at three different spatial scales. Results showed that in an unchanneled 0.024-ha headwater catchment, saturated and unsaturated infiltration from soil to bedrock is a dominant hydrological process at the soil-bedrock interface. Annual bedrock infiltration ranged from 35 to 55% of annual precipitation and increased as precipitation increased, suggesting a high level of potential bedrock infiltration, partly explained by the high buffering capacity of the soil layer overlying the bedrock. This physical property of the soil layer was an important factor in controlling the generation of bedrock infiltration and saturated lateral flow over the bedrock. In a 0.086-ha watershed including the unchanneled headwater catchment, exfiltration from the bedrock toward the soil layer composed more than half the annual discharge.