The adsorption and desorption of H-2 and Si2H6 on ion roughened Si (100) have been studied by temperature programmed desorption. In addition to reacting with surface dangling bonds, hydrogen can readily diffuse into the bulk and occupy defect sites after ion bombardment with an activation energy of 0.09 +/- 0.02 eV. The extent of surface roughness and bulk defects created by ion sputtering can be discriminated by adjusting the ion energy. At low ion energies (<100 eV), only surface roughness and near-surface bulk defects are present. Both monohydride and dihydride coverages increase after 50 eV ion sputtering compared with H-2 desorption from a smooth surface, implying an increased surface area due to ion roughening. However, only dihydride coverage increases with increased sputtering time. Because of the dramatically increased density of surface defects, adsorption probability of Si2H6 on the surface is greatly quenched after inert gas ion roughening.