The role that energetic (>800 eV) hydrogen ions play in inducing and modifying the formation of blisters in nanoscale Mo/Si multilayer samples is investigated. Such samples are confirmed to be susceptible to blistering by two separate mechanisms. The first is attributed to the segregation of H atoms to voids and vacancies associated with the outermost Mo layer, driving blister formation in the form of H2 filled bubbles. This process can occur in the absence of ions. A second blister distribution emerges when energetic ions are present in the irradiating flux. This is attributed to an ion-induced vacancy clustering mechanism that produces void blisters. The defects and strained states associated with the Mo-on-Si interfaces provide the preferred nucleation points for blistering in both cases. The effects of ions are ascribed to promotion of hydrogen uptake and mobility, in particular through the Si layers; to the generation of additional mobile species in the Si and Mo layers; and to the creation of new blister nucleation points. In addition to directly stimulating blistering via vacancy clustering, ions modify the development of H2-filled blisters. This is most evident in the formation of multi-component structures due to overlapping delaminations at different layer interfaces. This affect is attributed to the introduction of active transport of hydrogen from the H2 filled blisters across the outermost Mo-on-Si interface to the underlying layers. Ion-induced variations in hydrogen uptake and distribution and in the rates of blister nucleation and growth produce lateral differences in blister size and areal number density that create a macroscopic concentric pattern across the surface.