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Lake Tazawa, the deepest lake (423.4 m depth at maximum) in Japan underwent drastically changed water quality in 1940, because volcanic water from two active volcanos was then drawn into the lake for power generation and irrigation. Thereby, the pH of lake water decreased from 6.7 to 4.2, which exterminated a land-locked type of sockeye salmon, Oncorhynchus nerkakawamurae (locally called Kunimasu trout). Additionally, the mean residence time of lake water changed from 195 years to 8.9 years by rapidly increasing the outflow for power generation and irrigation. In this study, long-term chemical fluxes controlling lake water chemistry were obtained, and a groundwater water cycle system between the lake and the volcano was explored by estimating hydrological and chemical budgets of the lake. In the chemical budget estimate, two ionic species, SO42− and Cl−, in volcanic fluids were chosen and each mass conservation equation was yielded. The hydrological budget estimate gave us the net groundwater inflow at −1.36 m3/s on average over three periods in 2020–2021, and then the simultaneous equation coupled with the chemical budget equation allowed us to separate into groundwater inflow and outflow at 6.01 m3/s and 7.37 m3/s, averaged over the three periods, respectively. The evaluated groundwater inflow and outflow were compared with those of the other crater or caldera lakes. The linear relationship between the lake volume and the magnitude of groundwater inflow or outflow suggests that the groundwater cycle scale in such a lake increases with the magnitude of the volcanic eruption to have formed the lake.