In this work we examine the development of ion beam modified oxide-nitride-oxide structures formed by low-energy (1 keV) implantation of Si, N and Ar ions (1x1016 ions/cm2) into oxide-nitride gate stacks and subsequent wet-oxidation to form the blocking oxide. Transmission electron microscopy indicates that the thickness of the blocking oxide layer is strongly affected by the implantation process going from 1 nm (non-implanted sample) to 4-5 nm (N and Ar implants) and 7.5 nm (Si implant). The Si implanted stacks exhibit the highest attainable memory window (∼ 8.5 V for a 1 ms pulse regime), which involve both electron and hole storage. In contrast the thinner blocking oxide that develops to the nitrogen and argon implanted stacks limits the memory window which is due only to electron trapping. Room temperature charge retention measurements of the programming state reveal that the electron loss rate is faster in samples implanted with Si than N, allowing for a memory window of 1.7 V and 2.5 V respectively after ten years extrapolation. This retention behavior is mainly attributed to the different nature of the traps generated in the implanted materials.