This study evaluates the application of fluorinated graphene-based water desalination membranes using molecular dynamics simulations. The studied membranes are fluorinated nanoporous graphene oxide (F-NPGO) and nanoporous graphene (F-NPG) sheets. The applied pressure, as a driving force, was used in the range of 5-150 MPa in order to transfer the water molecules through the reverse osmosis (RO) membranes. The obtained results show that the water permeability of F-NPGO membranes (G1 and G2) is much greater than that of F-NPG membranes (G3 and G4) due to the existence of hydrophilic groups on their surface. The maximum value of water permeability was obtained for the G2 system (i.e., 3345 L/(m(2) hr bar)) at 150 MPa applied pressure. By fluorine functionalization of the pore edge, the passage of ions through the membrane, especially Cl- ions was prevented. This is the main issue of salt rejection performance. The minimum of obtained salt rejection percentage for F-NPGO membranes with the large pore (G2) was 94.31%, and small pore (G1) did not allow for crossing all of the ions. Many analyses such as water density map, water density profile, RDF, and PMF were computed for precisely understand and prove the performance of membrane systems.