Nanoporous graphene was proposed as an efficient material for reverse osmosis water desalination membranes because it allows water molecules to pass at high flux while rejecting hydrated salt ions. Nevertheless, from an experimental point of view it is still difficult to control the pore size. A scalable method to generate pores is urgently required for the diffusion of this technology. We propose, by theoretical calculations, an innovative and scalable strategy to better control the dimension of the pores in graphene-based membranes by reduction of single-layer graphene oxide (GO). The latter is first annealed at a controlled mild temperature to induce the aggregation of its randomly distributed oxygen-containing functional groups into small nanometric clusters. The layer then undergoes a high-temperature reducing treatment that causes the desorption of the functional groups along with carbon removal only in the oxidized areas, producing subnanometric pores while leaving unchanged the remaining pristine graphene areas.