The metallation of a tripodal ligand, hydrotris(3-methyl-2-thioxo-1-imidazolyl)borate with manganese(II) salt gave an unusual title compound, [Mn(H2O)(6)](C12H16N6BS3)(2).4H(2)O. The presence of soft donor atom in the borate moiety may be the cause of non-coordinating interaction with metal ion. The manganese(II) ion is coordinated with six water molecules leads to distorted octahedral geometry. In the crystal, the cations, anions and uncoordinated water molecules are linked by intermolecular O-H center dot center dot center dot O hydrogen bonds and week intermolecular O-H center dot center dot center dot S and C-H center dot center dot center dot S interaction, generating a three-dimensional network. The thermal behavior of the title compound was also investigated.