The scaling relationships of groundwater contributions have been examined in previous studies, but whether these findings are site‐specific or applicable to other watersheds remains unclear. Here, we illustrate how scaling relationships differ between watersheds with different geology. We investigated the spatial distributions of the specific discharge (discharge per unit drainage area) and chemical compositions of stream and spring water during baseflow periods in three Cretaceous to Eocene sedimentary watersheds and three Neogene volcanic watersheds in the Ishikari River basin, Japan. End‐member mixing analysis was used to separate stream water into shallow and deep groundwater. The specific discharge of stream water only significantly increased with drainage area for two of the volcanic study sites. Conversely, the ratio of deep groundwater to stream water only significantly increased with drainage area for two of the sedimentary study sites. The specific discharge of deep groundwater increased with area in both volcanic and sedimentary sites, but the specific discharge of shallow groundwater only increased with area for the volcanic sites. These findings indicate that the shallow groundwater flow played a crucial role in making geology‐dependent differences in scaling relationships. The geological effects on shallow groundwater flow were likely characterized by the spatial distribution of highly permeable bedrock layer. This geological control provides a useful framework for generalizing knowledge about the scaling relationships of groundwater contributions.