The Matsushiro earthquake swarm, which unusually persisted from 1965 to 1967, generated a gush of groundwater at the end of the period so massive that it was referred to as a “water eruption”. In this study, we analyze the geochemistry of Matsushiro spring waters collected in 2009 and 2010, with a focus on Li and Sr isotopic ratios. The Li and Sr isotopic ratios of Matsushiro spring waters, excluding the samples most contaminated by surface-water influence, were +4.0‰ to +6.0‰ for δ7Li and 0.7044–0.7045 for 87Sr/86Sr. These isotopic ratios are similar to those of Matsushiro igneous rocks (δ7Li –1.2‰ to 5.4‰, 87Sr/86Sr 0.7043–0.7050), supporting the hypothesis that the Matsushiro deep-derived fluid has a magmatic origin. Based on our results, the δ7Li value of Matsushiro deep-derived fluid without contamination by surface water is estimated to be +4.2‰. Using a Li isotope geothermometer, we estimate that the fluid–rock reaction temperature between the Matsushiro deep-derived fluid and magma exceeded 700°C. Furthermore, the insights obtained from this study on Matsushiro spring waters, emphasizing the characteristics of magma-derived fluid in central Japan, provide valuable information for distinguishing the origin of previously ambiguous fluid associated with the earthquake swarm at the southeastern foot of Ontake volcano, central Japan.