The process of stone recolonization by macroinvertebrates was studied at different spatial scales in a stream in Costa Rica. A hierarchical design was used with riffles nested into reaches, and individual stones nested into riffles. Macroinvertebrate abundance and taxon richness varied at riffle scale, although patterns of variation seemed to change with time of recolonization, and taxonomic composition varied mostly at reach scale. Patterns of variation of background communities and macroinvertebrate drift at different spatial scales suggest that the contribution of these two sources of colonists to stone recolonization depends on spatial scale. Macroinvertebrate abundance was related to local environmental variables during recolonization, but taxon richness was related to the local environment only in the very first stage of the process. The need for explicitly determining the appropriate spatial scale in the study of substrate recolonization is emphasized.