In this study, molecular dynamics simulations are used to investigate water transport mechanisms through hourglass-shaped pore structure in nanoporous boron nitride (BN) and graphene multilayers. An increase in water flux is evidenced as the gap between the layers increases, reaching a maximum of 41 and 43 ns(-1) at d = 6 angstrom in BN and graphene multilayers, respectively. Moreover, the BN multilayer exhibits less flux compared to graphene due to large friction force and energy barrier. In BN, the friction force dramatically increases when the layers are strongly stacked (d = 3.5 A), whereas it would be independent of the layer separation when the layers are sufficiently spaced (d >= 5 angstrom). In contrast, it was shown that the friction force is independent of the layer spacing in graphene. 04 the other hand, water molecules across the BN exhibits larger energy barriers compared to graphene when the layers: are highly spaced at d = 8 angstrom. Consistent with the result reported for the flux, the axial diffusion coefficient of water molecules in graphene increases with layer spacing, reaching a maximum of 6.8 X 10(-5) cm(2)/s when the layers are spaced at a, 6 angstrom.