Groundwater movements in volcanic mountains and their effects on streamflow discharge and representative elementary area (REA) have remained largely unclear. We surveyed the discharge and chemical composition of spring and stream water in two catchments: the Hontani river (NR) catchment (6.6 km2) and the Hosotani river (SR) catchment (4.0 km2) at the southern part of Daisen volcano, Japan. Daisen volcano is a young volcano (17 × 103 years) at an early stage of erosion. Our study indicated that deep groundwater that moved through thick lava and pyroclastic flows and that could not be explained by shallow movements controlled by surface topography contributed dominantly to streamflow at larger catchment areas. At the NR catchment, the deep groundwater contribution clearly increased at a catchment boundary defined by an area of 3.0 km2 and an elevation of 800 m. At the SR catchment, the contribution deep groundwater to the stream also increased suddenly at a boundary threshold of 2.0 and 700 m. Beyond these thresholds, the contributions of deep bedrock groundwater remained constant, indicating that the REA is between 2 and 3 km2 at the observed area. These results indicate that the hydrological conditions of base flow were controlled mainly by the deep bedrock groundwater that moved through thick lava and pyroclastic flows in the undissected volcanic body of the upper part of the catchment. Our study demonstrates that deep and long groundwater movements via a deep bedrock layer including thick deposits of volcanic materials at the two catchments on Daisen volcano strongly determined streamflow discharge instead of the mixing of small-scale hydrological conditions. Copyright © 2015 John Wiley & Sons, Ltd.