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 (N2) and methane (CH4) 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. An ultrathin and flexible carbon-based membrane for desalination can reject up to 96% of salt impurities with high flow rates. Amorphous carbon thin films have a mix of diamond-like and graphite-like chemical bonds that give rise to intriguing applications in semiconductors and designer coatings. Now, Morinobu Endo of Shinshu University in Japan and colleagues has developed a procedure to induce special nanostructure into amorphous carbon membranes for use in water treatment. The team formed sputtered carbon layers by using a mixture of argon, nitrogen and methane gases onto a porous ultrafiltration polymer film using a rapid, high-powered plasma technique. Desalination tests showed that this simple and scalable technique produced robust membranes with high salt rejection rates, particularly when nitrogen dopants were incorporated into the amorphous carbon structure. Nitrogen doping of nanostructured carbon-based membranes allows to produce ultrathin reverse osmosis membranes, which exhibit high robustness for water desalination applications. Structural and chemical characterization, water permeation and salt rejection tests, and computational modeling of these carbon-based membranes is discussed. Their salt rejection performance and degradation resistance reveal a strong dependency on the amount of nitrogen doping within the carbon structure. The properties shown by our nanostructured carbon membranes render them a potential alternative to current polymer-based membranes.