To fulfill the increasing demand for drinking water, researchers are currently exploring nanoporous two-dimensional materials, such as hexagonal boron nitride (hBN), as potential desalination membranes. A prominent, yet unsolved challenge is to understand how such membranes will perform in the presence of defects or surface charge in the membrane material. In this work, we study the effect of grain boundaries (GBs) and interfacial electrostatic interactions on the desalination performance of bicrystalline nanoporous hBN using classical molecular dynamics simulations supported by quantum−mechanical density functional theory (DFT) calculations. We investigate three different nanoporous bicrystalline hBN configurations, with symmetric tilt GBs having misorientation angles of 13.2, 21.8, and 32.2°. Using lattice dynamics calculations, we find that grain boundaries alter the areas and shapes of nanopores in bicrystalline hBN, as compared to the nanopores in monocrystalline hBN. We observe that, although bicrystalline nanoporous hBN with a misorientation angle of 13.2°shows an improved water flow rate by ∼30%, it demonstrates reduced Na + ion rejection by ∼6%, as compared to monocrystalline hBN. We also uncover the role of the nanopore shape in water desalination, finding that more elongated pores with smaller sizes (in 21.8-and 32.2°-misoriented bicrystalline hBN) can match water permeation through less elongated pores of slightly larger sizes, with a concomitant ∼3−4% decrease in Na + rejection. Simulations also predict that the water flow rate is significantly affected by interfacial electrostatic interactions. Indeed, the water flow rate is the highest when altered partial charges on B and N atoms were determined using DFT calculations, as compared to when no partial charges or bulk partial charges (i.e., charged hBN) were considered. Overall, our work on water/ion transport through nanopores in bicrystalline hBN indicates that the presence of GBs and surface charge can lead, respectively, to a decrease in the ion rejection and water permeation performance of hBN membranes.