Natural springs containing volcanic and magmatic components occur along major volcano-seismotectonic regions over the worlds. However, features of the deep-originated waters were less documented from regions where active volcanic and magmatic activities are not distributed. To characterize the presence of deep fluids of non-volcanic origin 28 groundwater samples (~ 1,230 m deep) were collected from hot spring sites located at western coast of Kumamoto where the typical subduction related magmatisms are absent. The samples were measured for dissolved ion concentrations and stable isotope ratios (δ2HH2O, δ18OH2O, δ13CDIC and δ34SSO4) that were compared with data of 33 water samples from vicinity surface systems. The groundwaters were classified into three types based on major hydrochemistry: high Cl− fluid, low concentration fluid, and high HCO3− fluid. Our dataset suggests that the high Cl− fluid was formed by saline water mixing with aquifer waters of meteoric origin and subsequently evolved by reverse cation exchange. The low concentration fluid is identical to regional aquifer water of meteoric origin that was subjected to cation exchange. The high HCO3− fluid showed the highest HCO3− concentrations (~ 3,888 mg/l) with the highest δ13CDIC (-1.9‰). Taking recent geophysical mappings under the study area, we suggest that dissolved carbon was of mantle origin and fluids with high HCO3− generated in lower crust were transported towards surface through structural weakness under open tectonic setting. Observed δ2HH2O and δ18OH2O shifts support this scenario. The occurrence of deep crustal fluid discharges was sporadic and limited in surface in the study area. Their impacts on surface hydrological systems were minimal except few locations.