Ultrathin, flexible and highly water-permeable nanostructured carbon (NC)-based membranes are formed on porous polymer supports by plasma high-power impulse magnetron sputtering in order to fabricate carbon-based membranes for water desalination. The carbon membranes are produced at room temperature using mixtures of argon (Ar), nitrogen (N 2 ) and methane (CH 4 ) as precursors, and this procedure constitutes a simple solvent-free, waste-free scalable process. Structural characterization, molecular simulation, water permeation and salt rejection assessments are used to correlate the performance and membrane structure. Molecular simulations indicate that nitrogen doping on the carbon-based membranes drastically modifies the pore distribution and avoids the formation of clustered regions of high-density carbons. The optimum NC-based membrane has up to 96% salt rejection rate for 0.2 wt% NaCl saline water, with high water permeability ca. 25 l m − 2 h − 1 MPa − 1 . The NC-based membranes as active layers for desalination membranes exhibit attractive characteristics which render them a potential alternative to current polymeric technology used in reverse osmosis processes.