Data on the dehydration of pentahydroborite, CaB2O(OH)6·2H2O and nifontovite, Ca3B6O6(OH)12·2H2O from the Fuka mine, Japan are presented. Critical temperatures of the dehydration of the borates were determined by thermogravimetric analysis/differential thermal analysis measurements. The untreated mineral samples and their heating products were investigated by X-ray diffraction and Raman spectroscopy. Upon dehydration, both minerals decompose and undergo amorphization, and at greater temperatures crystallize as an orthorhombic calcium borate, CaB2O4 (Pnca). The dehydration paths of the two minerals are different, with nifontovite showing a greater resistance to decomposition and amorphization than pentahydroborite. Differences in the dehydration processes are related to the residuals of the water content and structural accommodation of the borate polyanion.