Low energy Kr+ ions were used to create rough Si(100) surfaces. Hydrogen adsorption and desorption on these surfaces were studied using high resolution electron energy loss spectroscopy (HREELS) and temperature programmed desorption (TPD). A comparison of hydrogen TPD data from smooth and ion-roughened Si(100) surfaces showed no significant shift for the dihydride and monohydride related desorption features, revealing that ion impact roughening does not change the activation barriers for hydrogen desorption. In contrast to smooth Si(100), HREELS spectra from rough Si(100) surfaces with different hydrogen coverages showed a dihydride scissor mode at 0.8 ML and dihydride desorption below monolayer coverage in the corresponding TPD experiment. The vibrational spectra of hydrogen covered rough surfaces generally showed a smaller ratio of the scissor mode/bending mode intensity than the smooth Si(100) surfaces, suggesting a lower dihydride/monohydride coverage ratio. The corresponding TPD results on the other hand showed increased dihydride desorption and higher total coverages up to 2 ML. Although different dihydride units on terrace sites and at edge sites could not be unambiguously identified in the vibrational spectra, they provide a reasonable explanation for this inconsistency.