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Mountains are a source of water for downstream areas; thus, it is important to understand the storage and discharge characteristics of steep mountain catchments. Nested catchment studies have indicated that the relation between catchment area and specific discharge during baseflow can represent mesoscale storage and discharge characteristics, but this is poorly understood. We found that baseflow‐specific discharge increased with catchment size in the headwater of the Arakawa River and identified the processes responsible for this spatial pattern. Synoptic discharge measurements obtained in catchment areas of 0.05 to 93.58 km2showed that specific discharge increased more than threefold with increasing drainage area. Analyses of the spatial variation in precipitation, hydrographs from three continuous gauging stations, and isotopic tracers implied that in this catchment, considerable amounts of water infiltrated in bedrock on hillslopes and did not discharge into small streams, but instead fed surface flow into a larger downstream catchment. A review of previous nested studies demonstrated three spatial patterns for specific discharge: Specific discharge may increase or decrease with catchment area, or it may be independent of area. An increase in specific discharge with area was observed only in catchments with permeable bedrock, which implies that such an increase is a useful indicator of the importance of the bedrock flow path to mountain watershed storage. The pattern of relationships between catchment area and specific discharge can be used to assess the storage and discharge properties of mesoscale catchments when the processes driving each pattern have been clarified. Baseflow‐specific discharge increased more than threefold as catchment area increased from 0.05 to 93.58 km2in a steep headwaterA large amount of water infiltrated into bedrock in hillslopes in the headwater area and was only added to the river further downstreamStorage and discharge in mesoscale catchments can be assessed based on simple area baseflow‐specific discharge relationships