The formation of groundwater in the soil mantle has a dominant effect on rainwater discharge and shallow landslide occurrence in headwater catchments. Here, we report two completely different groundwater responses within a single well excavated into the soil mantle. One was an ephemeral-type response that is well described by physical hydrology models based on a geographic information system (GIS). The other was a semi-perennial-type response, rarely reported in previous studies, which cannot be explained by the existing physical models. The semi-perennial groundwater caused considerably high antecedent groundwater tables between storms, leading to an increased peak in the groundwater level during later heavy storm events and a likely increase in the risk of shallow landslides. Moreover, peaks in the semi-perennial groundwater lagged considerably behind rainstorm events, which probably affected base flow discharge by forming a delayed peak. Geochemical and geothermal observations indicated that the source of the semi-perennial groundwater was deep bedrock groundwater, demonstrating the considerable effects of bedrock groundwater on surface hydrological processes.