We report on the uptake of deuterium by thin-film Mo/Si multilayer samples as a result of exposure to fluxes of predominantly thermal atomic and molecular species, but also containing a small fraction of energetic (800–1000 eV) ions. These exposures result in blister formation characterized by layer detachment occurring exclusively in the vicinity of the Mo-on-Si interfaces. This localization is attributed to strained centers introduced within the interfacial region during silicide formation and subsequent Mo crystallization. The correlation between D-content and blistering was studied. After an initial uptake period the D-content stabilized at ~ 1.3 × 1016 at./cm2. Blister development is not simply a function of the content. Different blistering processes are simultaneously operative, with three distinct distributions being observed. The areal number densities of the initial two blister distributions to appear are established before the content stabilizes, while the multilayer is susceptible to successive stages of blistering associated with the effects of energetic ions. H-atom depth profiling of hydrogen-exposed samples by resonant nuclear reaction analysis shows preferential accumulation in the Mo layers. A distinct local maximum with a remarkably high hydrogen concentration (~ 19 at.%) develops in the outermost Mo layer. This is attributed to enhanced accommodation of hydrogen in voids and vacancies within the layer as a consequence of its polycrystalline structure and its highly-constrained state.