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The different physicochemical characteristics between volcano-hosted and fault-hosted on the Java island were determined. Boron isotope was applied to further distinguish the two geothermal systems. The possibility of a carbonate sedimentary basement as the host-rock of geothermal systems on the Bali island was investigated. The volcano-hosted had higher HCO3- contents and Mg/Na ratios compared the fault-hosted due to the CO2 magmatic gas supply. The reservoir temperature and lithium (Li) enrichment indicated a Quaternary magma and deep seated magma heat sources for the fault-hosted systems. Volcano-hosted geothermal system had a heavier Ã ´11B values than fault-hosted due to the magmatic fluids input and faster ascent. The (Ca2 Mg2 )/HCO3- of approximately 0.4 ruled out a carbonate host rock type on Bali, instead a calc-alkaline magmatic rocks was concluded. The well correlation of HCO3- content with Ca2 , Mg2 , Sr2 and K revealed water-rock interaction influenced by carbonic acid. B isotope confirmed seawater input in Parangtritis, Krakal and Banyuwedang.