Inorganic calcium carbonate precipitation from natural seawater and saline water at various pH values was carried out experimentally. The results show the clear positive relationships between boron concentration and δ11B of inorganic calcium carbonate with the pH of natural seawater and saline water. However, the variations of boron isotopic fractionation between inorganic calcite and seawater/saline water with pH are inconsistent with the hypothesis that B(OH)4- is the dominant species incorporated into the biogenic calcite structure. The isotopic fractionation factors α Between synthetic calcium carbonate precipitate and parent solutions increase systematically as pH increases, from 0.9884 at pH 7.60 to 1.0072 at pH 8.60 for seawater and from 0.9826 at pH 7.60 to 1.0178 at pH 8.75 for saline water. An unusual boron isotopic fractionation factor of larger than 1 in synthetic calcium carbonate precipitated from seawater/saline water at higher pH is observed, which implies that a substantial amount of the isotopically heavier B(OH)3 species must be incorporated preferentially into synthetic inorganic carbonate. The results propose that the incorporation of B(OH)3 is attributed to the formation of Mg(OH)2 at higher pH of calcifying microenvironment during the synthetic calcium carbonate precipitation. The preliminary experiment of Mg(OH)2 precipitated from artificial seawater shows that heavier 11B is enriched in Mg(OH)2 precipitation, which suggests that isotopically heavier B(OH)3 species incorporated preferentially into Mg(OH)2 precipitation.This result cannot be applied to explain the boron isotopic fractionation of marine bio-carbonate because of the possibility that the unusual environment in this study appears in formation of marine bio-carbonate is infinitesimal. We, however, must pay more attention to this phenomenon observed in this study, which accidentally appears in especially natural environment.