Deep-rooted fluids play important role in generating earthquakes and/or volcanic eruption, whereas it was difficult to research deep-rooted fluids from groundwater samples using traditional geochemical tools owing to contamination from surface water. The Li isotopic index, a new geofluid research tool, has a potential to provide us information about deep-rooted fluid without contamination from surface water. Based on the Li isotopic data of groundwater samples, it has been revealed that geofluid involving the earthquake swarms beneath the southeast flank of Ontake volcano in central Japan is attributed to non-volcanic deep-rooted fluid. Furthermore, this paper argues the relationship between inland large earthquakes and the discontinuous deep-seated fluid upwelling that is induced by the periodic breaking of the low-permeable barrier (cap) on the deep-seated fluid reservoir. The Li isotopic tool has a potential to provide us new information about the discontinuous deep-seated fluid upwelling.