Spent UO2 fuel will rapidly be altered to U6+ phases in nuclear waste repositories. Because most uranyl phases are based on sheet or chain structures and usually contain several molecular water groups, site-mixing, vacancies, as well as disorder in the orientation of hydrogen bonds may occur. A systematic survey of the published crystallographic data for uranates, uranyl oxide hydrates, phosphates, silicates, carbonates, and sulfates demonstrates that site-mixing apparently occurs in the structures of at least 31 uranyl phases. Calculations of the ideal site-mixing entropy indicate that the residual contribution that arises from substitution and vacancies to the third-law entropies of some uranyl phases is large. A brief examination of the crystal chemistry of water molecules in uranyl phases suggests that considerable residual entropy may be caused by the disorder of hydrogen bonds associated with interstitial H2O groups. In the geochemical environment that expected to occur in the near-field of nuclear waste repositories, the existence of structure-configurational entropy may reduce the uranium concentration of several log units in solutions equilibrated with some uranyl phases. Therefore, compositional analysis and structural determinations must be made on the samples used in calorimetric measurements, and the calorimetric data must be combined with solubility data to evaluate the thermodynamic stability of the interested phases.