Due to superior water permeability, structural stability, and adsorption capability, h-BN nanosheets are emerging as an efficient membrane for water desalination. In order to cater to the demand for potable water, large size membranes are required to maintain a high desalination rate from water purification systems. These large size membranes usually contain polycrystals with an offset in their mechanical properties from pristine h-BN nanosheets. In this article, molecular dynamics based simulations were performed in conjunction with a hybrid interatomic potential (reactive force field, TIP3P, and Lennard Jones) to simulate the mechanical strength of nanoporous single and bicrystalline h-BN nanosheets under water submerged conditions. The interaction between the atomic configuration of grain boundary atoms and nanopores in the presence of water molecules helps in investigating the viability of defective h-BN nanomembranes for underwater applications. Higher dislocation density enhances the mechanical strength of nanoporous bicrystalline h-BN nanosheets containing twin nanopores, which makes them a better substitute for water submerged applications as compared to the pristine nanosheets. The mechanical strength of nanoporous single crystalline h-BN nanosheets deteriorates with an increase in the number of nanopores, whereas a contrasting trend was observed with bicrystalline h-BN nanosheets.