Heuristic rules that allow identifying the preferred mixed‐valence isomers and Jahn‐Teller axis arrangements in the water oxidation catalyst [(Mn4O4)(V4O13)(OAc)3]n− and its activated form [(Mn4O4)(V4O13)(OAc)2(H2O)(OH)]n− are derived. These rules are based on computing all combinatorially possible mixed‐valence isomers and Jahn‐Teller axis arrangements of the MnIII atoms, and associate energetic costs with some structural features, like crossings of multiple Jahn‐Teller axes, the location of these axes, or the involved ligands. It is found that the different oxidation states localize on different Mn centers, giving rise to clear Jahn‐Teller distortions, unlike in previous crystallographic findings where an apparent valence delocalization was found. The low barriers that connect different Jahn‐Teller axis arrangements suggest that the system quickly interconverts between them, leading to the observation of averaged bond lengths in the crystal structure. We conclude that the combination of cubane‐vanadate bonds that are chemically inert, cubane‐acetate/water bonds that can be activated through a Jahn‐Teller axis, and low activation barriers for intramolecular rearrangement of the Jahn‐Teller axes plays an essential role in the reactivity of this and probably related compounds.