Understanding the mechanism of ion rejection in the separation process remains a major hurdle in designing new membrane materials for seawater desalination. Here, we investigate the effects of water and aromatic polyamide (PA) membrane on the rejection of salt ions, such as Fe2+, Na+, and Cl-, by molecular dynamic simulations. Results demonstrate that water plays a key role in salt ion rejection because salt ions preferentially interact with water molecules to form hydrates with multishell structures, which aids the rejection of various salt ions. For FeCl2 aqueous solution, the innermost shell water molecules of a Fe2+ hydrate can hardly be replaced by other substances in their molecular dynamics simulations, so ions would be highly rejected if the effective diameter of a water channel (EDC) in the membrane is smaller than that of the innermost shell of a hydrate. However, the water molecules in the second water shell can be replaced by the atoms of the membrane when the EDC is smaller than the size of the second shell (about 9 angstrom). Besides, although the sizes of these ions approximate to those of water molecules, the rejection level of PA membrane to salt ions is higher than that to water, which is accounted for by the formation of hydrate. POLYM. ENG. SCI., 55:466-473, 2015. (c) 2014 Society of Plastics Engineers