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Recent seismic monitoring mainly by the Hi-net High sensitivity seismograph network in Japan for the last decade has been revealing the 3D structure of velocity anomaly in the crust and mantle due to heterogeneous presence of deep-seated fluids and fluid-related deep low frequency earthquakes in subduction zones of Japan arc. Petrological water circulation models combined with geophysical subduction models quantitatively show the water budget in the solid earth. The recent findings infer the importance of deep hydrothermal fluid on the occurrence of inland earthquakes. As the models are built with the result obtained by monitoring, experimental techniques or simulations, implications from evidence-based geochemical and geological studies are expected for the proof of water circulation models. Hence, we examined chemical features of deep groundwaters in SW Japan arc, and showed spatial distribution of deep-seated fluid mixed into groundwater. We found that the deep-seated fluid, whose isotopic composition is similar to magmatic, has the high Li/Cl ratio 0.001 in wt. ratio and concluded that Li/Cl is a good indicator for detecting the slab-related deep-seated fluid in groundwaters. Spatial distribution of Li/Cl reveals that slab-related deep-seated fluid upwells along the faults and tectonic lines, and at close to Quaternary volcanoes in SW Japan arc. In most cases, upwelling places are found close to the areas where deep low frequency DLF earthquakes are occurring, implying that deep-seated fluid causes DLF events.