In this work, molecular dynamics simulations were used to determine the surface tension profile of water on graphene and boron nitride (BN) multilayers and to predict water permeation through nanoporous graphene and BN membranes. For both graphene and BN multilayers, a decrease in surface tension (γ) was evidenced as the number of layers increased. This lessening in γ was shown to result from a negative surface tension contribution due to long-range wetting of water, which also contributes to lower water permeation through a two-layer membrane with respect to permeation through a monolayer. We also showed that a decrease in water surface tension on a BN monolayer with regards to graphene was at the origin of an increase in water permeation through BN. Our findings suggest that nanoporous BN membranes could be attractive candidates for desalination applications.