Adsorption and isotopic fractionation of boron on clastic sediment is one process responsible for the heavy boron isotopic composition of the modern ocean. However, the mechanism by which boron complexes to the surface of clay minerals and the cause of its isotopic fractionation are still unclear. We performed two sets of experiments, using solutions of pure water with added boron and seawater, to explore the isotope behavior during adsorption of boron onto kaolinite, smectite and illite. The dataset consists of an excel file with four sheets that store (1) the NIST RM 803 measurements we used to establish the long-term reproducibility of our isotope measurements, (2) results of our pure experiment, (3) results of our seawater experiments and (4) a global compilation of XRD-based riverine clay mineral assemblages.