Functionalized nanoporous graphene has shown great promise as emerging membrane. Herein, we computationally demonstrate the separation performance using pyridinic-like nitrogen doped nanoporous graphene as reverse osmosis desalination membrane. The water permeation and salt rejection of the functionalized graphene membranes with various nitrogen-doping levels were simulated and characterized. We show that all functionalized graphenes investigated in this work exhibit higher water Flux and acceptable salt rejection. In particular, the NOH graphene membrane with partial hydroxyl group inclusion shows excellent desalination efficiency. The interfacial properties of water and ions, as well as their free energy landscapes in passing through the graphene nanopores have been simulated in order to explore the desalination mechanism. The moderate free energy barriers for water passages confirm larger water fluxes in the functionalized graphene membranes. It was revealed that the salt rejection for the functionalized graphenes is the pore size exclusion of hydrated ions and the charged repulsion from pore surfaces is not the main factor. Overall, our results indicate that pyridinic-like nitrogen doped graphenes have a significant potential as nanostructured desalination membranes. (C) 2015 Elsevier B.V. All rights reserved.