While single-layer nanoporous graphene (NPG) has shown promise as a reverse osmosis (RO) desalination membrane, multilayer graphene membranes can be synthesized more economically than the single-layer material. In this work, we build upon the knowledge gained to date toward single-layer graphene to explore how multilayer NPG might serve as a RO membrane in water desalination using classical molecular dynamic simulations. We show that, while multilayer NPG exhibits similarly promising desalination properties to single-layer membranes, their separation performance can be designed by manipulating various configurational variables in the multilayer case. This work establishes an atomic-level understanding of the effects of additional NPG layers, layer separation, and pore alignment on desalination performance, providing useful guidelines for the design of multilayer NPG membranes.