Molecular dynamics simulation using COMPASS force field has been employed to understand the dynamics of water diffusion and structuring in silicalite-1 and Na-ZSM-5 (Si/Al = 95 and 191) samples at three different temperatures, 297, 354, and 393 K, at a water loading of 8 molecules per unit cell, in canonical ensemble. Diffusion coefficients were significantly reduced upon the introduction of aluminum atoms into the framework, together with charge balancing cations placed in their vicinity, since the ion-dipole interactions dominant in ZSM-5 samples are stronger than the H-bond interactions in silicalite-1. The activation energy of diffusion increased with decreasing Si/Al ratio. In the silicalite-1 and ZSM-5 samples, straight channels were observed to be preferred than the sinusoidal ones and the channel preference was not observed to be a strong function of either temperature or the Si/Al ratio. The ordered structures of the water molecules, forming clusters in the channels of silicalite-1 at low temperature was observed to be broken to some extent by increased temperatures, and decreased Si/Al ratio, resulting in less ordered structures. The positions of the water molecules in the straight and sinusoidal channels for the ZSM-5 samples were mainly determined by the location of the charge compensating cation(s) in the structure, as was shown by the concentration profiles.