Despite the success of reverse osmosis (RO) for water purification, the molecular-level physico-chemical processes of contaminant rejection are not well understood. Here we carry out non-equilibrium molecular dynamics (NEMD) simulations on a model polyamide RO membrane to understand the mechanisms of transport and rejection of both ionic and inorganic contaminants in water. While it is commonly presumed that the contaminant rejection rate is correlated with the dehydrated solute size, this approximation does not hold for the organic solutes and ions studied. In particular, the rejection of urea (2.4 angstrom radius) is higher than ethanol (2.6 angstrom radius), and the rejections for organic solutes (2.2-2.8 angstrom radius) are lower than Na+ (1.4 angstrom radius) or Cl- (2.3 angstrom radius). We show that this can be explained in terms of the solute accessible intermolecular volume in the membrane and the solute-water pair interaction energy. If the smallest open spaces in the membrane's molecular structure are all larger than the solute size including its hydration shell, then the solute-water pair interaction energy does not matter. However, when the open spaces in the polymeric structure are such that solutes have to shed at least one water molecule to pass through a portion of the membrane molecular structure, as occurs in RO membranes, the pair interaction energy governs solute rejection. The high pair interaction energy for water molecules in the solvation shell for ions makes the water molecules difficult to shed, thus enhancing the rejection of ions. On the other hand, the organic solute-water interaction energies are governed by the water molecules that are hydrogen bonded to the solute. While these hydrogen bonds have pair interaction energies that are much larger than that of the non-hydrogen bonded water molecules in the solute solvation shell, they are significantly less than the ion-water pair interaction energy. Thus, organic solutes more easily shed water molecules than ions to pass through the RO membrane. Since urea molecules have more hydrogen-bonding sites than alcohol molecules, urea forms more hydrogen bonds with the membrane polymer chains leading to a higher rejection of urea than occurs for ethanol, a molecule of similar size but with fewer hydrogen bonding sites. These findings underline the importance of the solute's solvation shell and solute-water-membrane chemistry in the context of reverse osmosis, thus providing new insights into solute transport and rejection in RO membranes. (C) 2016 Elsevier B.V. All rights reserved.