The early Pliocene Shirahama Limestone is a grainstone-packstone principally composed of fragments of algae, bryozoa, and echinoderm and subordinate volcanic rocks. The limestone was variously dolomitized and the regional distribution of dolomite is patchy. Dolomite occurs as isolated crystals filling pores, moulds, and solution vugs, and mosaic aggregates replacing bioclasts. Calcite occurs as rim and pore-filling sparry cements, and as calcareous skeletons. Isotopically, the dolomites are classified into a heavy oxygen group (−2 to − 3.5%0 PDB) and a light oxygen group (−5.5 to − 7.5%0 PDB). Calcite associated with heavy oxygen dolomite has δ18O of − 6.5 to −8.5%0 PDB, whereas those associated with light oxygen dolomite have a wide range from −7.5 to −14%0 PDB. Calcite in dolomite-free limestone has an oxygen isotopic composition of −2 to −8.5%0 PDB. Textures, chemistry, and isotopic evidence indicate that heavy oxygen calcite formed in freshwater, and heavy oxygen dolomite in a meteoric-marine mixture of 10–30% seawater. Light oxygen calcite and dolomite precipitated from modified hydrothermal fluids at approximately 30–65°C.
Petrographic features, and both isotopic and chemical evidence suggest that the Shirahama Limestone was exposed to freshwater soon after deposition. Subsequently blocky calcite precipitated (Stage I). The limestone was locally submerged in the meteoric-marine mixture due to gradual subsidence or eustatic movement. This led to the precipitation of heavy oxygen, zoned dolomite and dolospar (Stage II). Hydrothermal alterations occurred in the area a few Myr ago, and related hydrothermal fluids and mixed meteoric-hydrothermal waters caused dedolomitization of some zoned dolomite, partial dissolution of vuggy dolomite, precipitation of limpid dolomite and recrystallization of some earlier dolomites (Stage III). Zeolites were also precipitated from these fluids. Finally, the Shirahama Limestone was exposed again to freshwater and sparry calcite precipitated to plug some of the remaining pores (Stage IV).