Montmorillonite (Mt) expansion and swelling are key factors determining the barrier performance of bentonite in trans-uranic (TRU) and high-level radioactive waste disposal. In the case of co-located geological disposal of TRU and high-level waste, NH4+ ions formed from NO3− ions leached from TRU waste may contact bentonite, exchanging with interlayer cations of Mt. to form NH4-Mt, with a reduction in barrier performance. Because of the similar hydration energies of NH4+ and K+, NH4-Mt may have less expandability or even change to a non-expandable mineral such as K-Mt. An understanding of the expansion and alteration behavior of NH4-Mt, especially in comparison with K-Mt, is thus necessary in waste-disposal safety assessment. Here, the hydration behavior of NH4-Mt was investigated by X-ray diffraction (XRD) analysis and molecular dynamics (MD) simulation and compared with that of K-Mt. XRD profiles under relative humidity (RH) control indicate that expansion of NH4-Mt is similar to that of K-Mt at >40% RH with slightly different d-values. However, NH4-Mt expansion is kept at ∼20% RH, while K-Mt tends to dehydrate. MD simulations indicate that hydrogen bonding with NH4+ ions causes the differences in hydration behaviors of NH4- and K-Mt, increasing basal spacing in dehydrated states and promoting hydration. This “hydration gap” may be attributed to differences in alteration to non-expandable minerals by dehydration, with NH4+ having less tendency for alternation and less of an effect on the barrier performance of bentonite than K+.