A H₄B₄O₉²⁻ ion which makes up the (NH₄)₂B₄O₅(OH)₄·2H₂O crystal structure has two types of boron–oxygen bonds, i.e. single B–O bonds and an intermediate between single and double BO bonds. Differences between these two bond types are visible not only because they differ by their lengths but also a topology of electron density distribution differs. This also gives a hint as to how to distinguish between these two bond types. Experimental results based on multipole model refinement gave excellent agreement with theoretical calculations and literature data. Calculations at bond critical points for B–O and BO (electron density, the Laplacian of electron density and the localized-orbital locator function) suggest us how boron–oxygen bonds should be categorised with respect to compounds previously reported in the literature. Additionally, a novel synthesis method for the investigated compound has been developed, which involves crystallization from an aqueous solution of BH₃NH₃ dissolved in a mixture of tetrahydrofuran and water.