Despite the importance of boron as a proxy of past ocean pH, the crystal-chemical factors controlling its incorporation in the structure of calcium carbonates are still poorly understood. This is partly linked to an imperfect knowledge of the coordination, protonation state and local environment of boron species in these minerals. In the present study, we use first-principles quantum mechanical tools to model selected trigonal and tetragonal boron species in calcite and aragonite. The stable geometry of the models is obtained from standard energy minimization schemes or using a more advanced metadynamics exploration of their configurational space. The computation of 11B NMR chemical shifts and quadrupolar coupling parameters enables a straightforward comparison of the models to existing experimental NMR data. The results show that B in calcium carbonates does occur as structural species substituted for CO32− anions. The B speciation depends on the polymorph considered. In calcite, structural boron is present as partially deprotonated trigonal BO2(OH)2− species coexisting with a fraction of substituted B(OH)4− groups. In aragonite, the B(OH)4− substitution for CO32− anions is dominant. Different species, including entrapped B(OH)3 molecules and substituted BO33− groups also occur in biogenic samples. The diversity of B speciation reflects a diversity of B incorporation mechanisms and sheds light on previous studies confronting B isotopic composition determination with NMR observations. The mechanisms of boron incorporation in calcium carbonates are probably more complex than usually assumed in the literature using boron isotopes as a proxy of paleo-atmospheric CO2 reconstructions. Although not invalidating the empirical paleo-pH proxy, these results call for a better understanding of the fundamental mechanisms of boron incorporation in carbonates.