By the deliberate choice of the internal ligands of the porous nanocapsules [{(Mo)Mo(5)}(12){Mo(2)(ligand)}(30)](n-), the respective cavities' shells can be differently sized/functionalized. This allows one to trap the same large number of water molecules, that is, 100 in a capsule cavity with formate ligands having a larger space available, as well as in a cavity containing sulfates and hypophosphites, that is, with less space. Whereas the 100 molecules fill the space completely in the second case in which they are organized in three shells, a four-shell system with underoccupation and broken hydrogen bonds is observed in the other case. This is an unprecedented result in terms of the structurally well defined special forms of "higher and lower density" water molecule assemblies. Precisely, by replacing the larger ligands in the mentioned nanocapsule type by formates, voids in the capsule cavity of (HC(NH(2))(2))(22)[{(HC(NH(2))(2))(20)+(H(2)O)(100)} subset{(Mo)Mo(5)O(21)(H(2)O)(6)}(12){Mo(2)O(4)(HCO(2))}(30)]ca. 200 H(2)O are generated that get filled with water molecules concomitant with an expansion of the three to four shell {H(2)O}(100) cluster. The water shells in both capsules containing different ligands are organized in the form of dodecahedra (partly with underoccupation) and a strongly distorted rhombicosidodecahedron spanned by a {H(2)O}(60)={(H(2)O)(5)}(12) aggregate. The well-defined water shells only emerge if cations cannot enter into the capsules, which is achieved by closing the pores with plugs/guests such as formamidinium cations. The work is based on the syntheses of two new compounds, related single-crystal X-ray diffraction studies, and molecular dynamics simulations, which show remarkably that water molecule shell structuring occurs in the capsules due to the confined conditions even in the case of open pores and at room temperature if cation uptake is prevented.