The influence of molecular water on the structure and formation of silica clusters is modeled with the use of the MMH (multiple minima hypersurfaces) approach. It combines quantum chemical Hamiltonians for the calculation of the internal energy with statistical modeling and formulas for the calculation of thermodynamic functions of association. The structures of the most probable clusters of hydration and some properties of the association with water are proposed. Different simple structures are calculated to consider the entropy of association in place of the simpler approach of a single "global minimum". Ab initio, DFT, and semiempirical calculations of the structures and relevant reactions of silica fragments are also reported, confirming the reliability of the results on very different grounded quantum mechanical methods. Particularly, it has been shown that semiempirical PM3 Hamiltonian is reliable for silica cluster calculations of this kind, in comparison with accurate ab initio SCF and other DFT calculations. Apparently, the well-known systematic failures of this Hamiltonian are absent in this kind of structures and interactions. The increasing hydrophobic character of neutral silica clusters appears as a result of the free energies of association, and therefore, it originates on entropy. It is remarkable that the simple global minimum approach currently used in works of molecular modeling on this kind of compounds, where several hydrogen bridges have a place to exist with several different conformations, must be taken with caution given the remarkable entropy of association of such systems.