The title compound, [Mn(C12H15NO5)2]·0.39H2O, is a 0.39 hydrate of the isostructural complex bis(2-{[1,1-bis(hydroxymethyl)-2-oxidoethyl]iminomethyl}-6-methoxyphenolato)manganese(IV) that has previously been reported by Back, Oliveira, Canabarro & Iglesias [Z. Anorg. Allg. Chem.(2015),641, 941–947], based on room-temperature data. The current structure that was determined at 100 K reveals a lengthening of theccell parameter compared with the published one due to the incorporation of the partial occupancy water molecule. The title compound crystallizes in the tetragonal chiral space groupP41212; the neutral [MnIV(C12H15NO5)2] molecule is situated on a crystallographicC2axis. The overall geometry about the central manganese ion is octahedral with an N2O4core; each ligand acts as a meridional ONO donor. The coordination environment of MnIVat 100 K displays a difference in one of the two Mn–O bond lengths, compared with the room-temperature structure. In the crystal, the neutral molecules are stacked in a helical fashion along thec-axis direction.