We have conducted a comparative computational investigation of the molecular structure and water adsorption properties of molybdenum oxide and sulfide clusters using density functional theory methods. We have found that while Mo3O6- and Mo3S6- assume very similar ring-type isomers, Mo3O9- and Mo3S9- clusters are very different with Mo3O9-having a ring-type structure and Mo3S9- having a more open, linear-type geometry. The more rigid angle (Mo-S-Mo) bond angle is the primary geometric property responsible for producing such different lowest energy isomers. By computing molecular complexation energies, it is observed that water is found to adsorb more strongly to Mo3O6- than to Mo3S6-, due to a stronger oxide-water hydrogen bond, although dispersion effects reduce this difference when molybdenum centers contribute to the binding. Investigating the energetics of dissociative water addition to Mo3X6- clusters, we find that, while the oxide cluster shows kinetic site-selectivity (bridging position vs terminal position), the sulfide cluster exhibits thermodynamic site-selectivity.