This study investigated runoff to clarify the effect of bedrock groundwater dynamics on runoff generation processes in granodiorite headwater catchments (NA and NB) located in the western Tanzawa Mountains, Central Japan. The rainfall-runoff response and water balance calculated using the hydrological cycle (HYCY) model with outflow were also analyzed based on the observed precipitation, runoff, and bedrock groundwater level (at a depth of 50 m). In 2013, the annual runoff rate was 398 mm (21% of the rainfall) in NA and 1209 mm (63% of the rainfall) in NB, respectively. The bedrock groundwater level varied for approximately 3 m, and responded to 30-mm rainfall events. The significant relationship between the base flow and bedrock groundwater level indicated that the bedrock groundwater markedly influenced base flow generation. The calculated annual bedrock infiltration values of 656 mm (34% of the rainfall) in NA and 52 mm (3% of the rainfall) in NB significantly influenced the runoff rate. Our results demonstrated that significant and negligible amounts of bedrock groundwater infiltration were observed, even in neighboring catchments. Those bedrock groundwater dynamics significantly influenced the observed differences in the runoff rate and base flow generation. KEYWORDS runoff; bedrock groundwater infiltration; granodiorite; HYCY model with outflow; Tanzawa Mountains