The application of hydrogen flooding was recently shown to be a simple and effective approach for improved layer differentiation and interface determination during secondary ion mass spectrometry (SIMS) depth profiling of thin films, as well as an approach with potential in the field of quantitative SIMS analyses. To study the effects of hydrogen further, flooding of H2 molecules was compared to reactions with atomic H on samples of pure metals and their alloys. H2 was introduced into the analytical chamber via a capillary, which was heated to approximately 2200 K to achieve dissociation. Dissociation of H2 up to 30% resulted in a significant increase in the intensity of the metal hydride cluster secondary ions originating from the metallic samples. Comparison of the time scales of possible processes provided insight into the mechanism of hydride cluster secondary ion formation. Cluster ions presumably form during the recombination of the atoms and molecules from the sample and atoms and molecules adsorbed from the gas. This process occurs on the surface or just above it during the sputtering process. These findings coincide with those of previous mechanistic and computational studies.