Although there has been growing interest in the effect of dispersal on species diversity, much remains unknown about how dispersal occurring at multiple scales influences diversity. We used an experimental microbial landscape to determine whether dispersal occurring at two different scales – among local communities and among metacommunities – affects diversity differently. At the local scale, dispersal initially had a positive effect and subsequently a neutral effect on diversity, whereas at the metacommunity and landscape scales, dispersal showed a consistently negative effect. The timing in which dispersal affected beta diversity also differed sharply between local communities and metacommunities. These patterns were explained by scale- and time-dependent effects of dispersal in allowing spread of species and in removing spatial refuges from predators. Our results suggest that the relative contribution of opposing mechanisms by which dispersal affects diversity changes considerably over time and space in hierarchical landscapes in which dispersal occurs at multiple scales.