Polyamide (PA) membranes possess properties that allow for selective water permeation and salt rejection, and these are widely used for reverse osmotic (RO) desalination of sea water to produce drinking water. In order to design high-performance RO membranes with high levels of water permeability and salt rejection, an understanding of microscopic PA membrane structures is indispensable, and this includes water transport and ion rejection mechanisms on a molecular scale. In this study, two types of virtual PA membranes with different structures and densities were constructed on a computer, and water molecular transport properties through PA membranes were examined on a molecular level via direct reverse/forward osmosis (RO/FO) filtration molecular dynamics (MD) simulations. A quasi-non-equilibrium MD simulation technique that uses applied (RO mode) or osmotic (FO mode) pressure differences of several MPa was conducted to estimate water permeability through PA membranes. A simple NVT (Number, Volume, and Temperature constant ensemble)-RO MD simulation method was presented and verified. The simulations of RO and FO water permeability for a dense PA membrane model without a support layer agreed with the experimental value in the RO mode. This PA membrane completely rejected Na+ and Cl− ions during a simulation time of several nano-seconds. The naturally dense PA structure showed excellent ion rejection. The effect that the void size of PA structure exerted on water permeability was also examined.