A substrate of a non-volatile storage system includes selected regions in which additional ions are deeply implanted during the fabrication process. NAND strings are formed over the selected regions such that end word lines of the NAND strings are over the deeply implanted ions. The presence of the deeply implanted ions below the end word lines increases a channel capacitance of the substrate under the end word lines. Due to the increased capacitance, boosting of a channel in the substrate below the end word lines is reduced, thereby reducing the occurrence of gate induced drain leakage (GIDL) and band-to-band tunneling (BTBT) and, consequently, program disturb. A shallow ion implantation may also be made to set a threshold voltage of storage elements of the NAND string.