The effect of functionalized nanoporous boron nitride nanosheet (BNNS) membranes was investigated for salt separation from sea water by molecular dynamics simulations. For this purpose, a pore was created in the BNNS membrane and functionalized with various chemical functions such as hydrogen (-H), fluorine (-F), and hydroxyl (-OH) group. Functionalized membrane was placed in the middle of the simulation box in an aqueous ionic solution containing Na+ and Cl- ions. For salt rejection, an external pressure was applied to the simulation box. In this work, water permeability and salt rejection were obtained for four different systems at pressure range of 10-100 MPa. Potential of mean force of water molecules, Na+ and Cl- ions were calculated to explain the transport of water molecules and ions through the functionalized pore of BNNS membrane. Also, the water density, radial distribution functions of water-water and ion-water, hydrogen bonds, water density map, and number of water molecules inside the pore of membrane were obtained. The results demonstrated that the hydrophilic chemical functions such as -F and -OH group can improve the water permeability even at low pressures.