We report the surface modification of nanochannels whose channels are formed from stacked and overlapping graphene oxide sheets, in which the high density of nitrogen/oxygen groups and networks of H bonds serve as excellent proton channels but block the transport of cations such as Li+ and Na+. The membrane has excellent stability when immersed for long periods under water and has an NaCl rejection rate of approximately 99% while maintaining permeability to water and performs well for at least 400 h for desalination. Our straightforward approach to achieving this type of two-dimensional channel material for selective ion conduction, efficient ion separation, and water desalination might open a host of possible new uses.