Changes in natural habitats and the community response to such changes have important impacts on the distribution of diversity. Theoretical advances have highlighted the importance of including dispersal traits to predict responses to habitat loss but there is a lack of empirical evidence. We investigated the effect of metacommunity size (by manipulating the number of habitat patches) and isolation (by manipulating proximity to reefs) in structuring marine macrofaunal communities. The overall response of macrofauna to changes in habitat size and proximity to reefs varied according to the species’ ability to disperse after settlement. Whilst the richness of species with sessile adult stages responded to proximity to reefs in which metacommunities were deployed, species with motile adult stages responded to metacommunity size. Results were similar at both the patch- and metacommunity scales. A subsequent experiment showed that colonisation had an impact on the macrofaunal responses to reef proximity, which persisted throughout the community assembly process. The inclusion of simple functional traits (i.e. post-settlement dispersal) allows a better understanding of species responses to the spatial configuration of habitats at multiple ecological scales, which may be key for predicting the consequences of habitat loss.