In this study, we examined the specific flow rate and electrical conductivity during various periods without rainfall in 16 watersheds of the Oigawa River system in Shizuoka Prefecture, Japan. The aim was to explore the connection between the geological structure and the spatial variability of rainfall‐runoff in a mountainous region characterized by high relief and composed of accretionary sedimentary rock from the Paleozoic and Mesozoic Eras. We assessed three different geological structural conditions within these watersheds: dip slope, anti‐dip slope, and strike‐direction slope. The findings revealed that there was no evident correlation between the specific flow amount and the specified geological conditions of the watershed. However, in watersheds dominated by dip slopes, it is implied that the storage capacity is reduced, leading to a quicker response in rainfall‐runoff. Moreover, these areas exhibit a higher contribution of rainwater runoff through the deeper bedrock layers.