The nondestructive investigation of single vacancies and vacancy clusters in ion-irradiated samples requires a depth-resolved probe with atomic sensitivity to defects. The recent development of short-pulsed positron beams provides such a probe. Here, we combine depth-resolved Doppler broadening and positron annihilation lifetime spectroscopies to identify vacancy clusters in ion-irradiated Fe and measure their density as a function of depth. Despite large concentrations of dislocations and voids in the pristine samples, positron annihilation measurements uncovered the structure of vacancy clusters and the change in their size and density with irradiation dose. When combined with transmission electron microscopy measurements, the study demonstrates an association between the increase in the density of small vacancy clusters with irradiation and a remarkable reduction in the size of large voids. This, previously unknown, mechanism for the interaction of cascade damage with voids in ion-irradiated materials is a consequence of the high porosity of the initial microstructure.