Molecular dynamics simulations were conducted to evaluate the effect of water desaturation on ions and water density distribution and diffusion properties in a clay mineral mesopore. Simulations were carried out using the Polarizable Ion Model (PIM) force field. Desaturation of the pore was responsible for significant changes in localization and mobility of water molecules and ions, especially in most unsaturated conditions, for which charge overcompensation by cations adsorbed on the surface through inner-sphere complexes were observed. While cations and anions mobility decreased monotonously with increasing desaturation, pore-averaged diffusion coefficient of water molecules exhibited a complex evolution with an increased diffusion coefficient value at low desaturation level, and then a drop of this value at high desaturation level. Water diffusion was influenced by two antagonistic processes, i.e. acceleration of water molecules diffusion at water/air interface; and slowdown at water / clay mineral interface. These observations can be put in perspective with differences in macroscopic diffusion properties among cationic, anionic and water tracers observed in experiments conducted on desaturated clay mineral rock samples.