Abstract To elucidate the early diagenesis of carbonates, a hydrogeochemical study was carried out on groundwater in shallow-marine Pleistocene limestones on Irabu Island, southwestern Japan. Carbonate diagenetic processes and porosity changes within vadose, freshwater phreatic, and mixing zones were determined on the basis of hydrogeochemical analyses. Net dissolution of limestone occurs mainly in the vadose and upper mixing zones where dissolution results in an increase in porosity of 1.98% per 10 k.y. and 2.10% per 10 k.y, respectively. Calcite precipitation occurs in the upper 1.5 m of the freshwater phreatic zone, and causes a decrease in porosity of 5.36% per 10 k.y. Significant dissolution and precipitation apparently do not occur in the middle to lower part of the freshwater phreatic zone, even though that zone has active groundwater flow. The main factor controlling diagenetic reactions on Irabu Island is considered to be CO 2 fluxes into the groundwater system. Differences in solubility of carbonate minerals are not significant for the diagenesis on Irabu Island because the island is composed almost entirely of low-Mg calcite.