The importance of the substratum to benthic species can vary depending on the material of its construction. Intertidal boulder reefs with different rock types often have distinct benthic assemblages, and their ecology is structured strongly by succession. Therefore, dynamics causing assemblage variability may involve an interaction of factors involved in succession with features of the substratum. The current experiments monitored 11 month successional trajectories of benthic invertebrates on 2 rock types (siltstone and limestone) with differing physical characteristics. Unmanipulated boulders in siltstone and limestone reefs had different assemblages, but when bare boulders of the non-native rock type were transplanted into reefs, assemblages developing on non-native boulders were in most ways similar to those on boulders of the reef's native rock type. A substratum-dependent variation in successional trajectories was observed for one taxon, the true limpet Notoacmea spp. Under specific conditions of rock type at the individual boulder scale and the wider reef scale, evidence was found of a consistent peak in abundance during early succession. Notoacmea spp. was also positively associated not only with siltstone reefs but also with individual siltstone boulders, suggesting an effect of rock type at the boulder scale. Although processes occurring at scales encompassing whole reefs mostly dictate how these assemblages are associated with rock type, some species are affected by rock type at the boulder scale, and the effect can vary during succession. For such species, successional processes and environmental factors need to be considered synergistically to understand spatial and temporal population variability.