The composition of meiobenthic and macrobenthic communities between different intertidal reef-flat pools on Rocas Atoll (South Atlantic) was compared, and related to properties of the carbonate sediments and patterns of reef growth. Both univariate and multivariate statistical analyses showed that the reef height and size influenced the properties of the reef-derived sediments and were correlated with the composition and abundance of the benthic fauna in the intertidal pools. The temperature and the salinity between Rocas tidal flat reef pools did not vary significantly, despite the differences in size, exposure degree and elevation, suggesting that percolation through the porous lime body of the reef and/or the connection between the tidal pools and seawater by blowholes have a significant effect on the tidal pools. The major asymmetry in the reef topography of Rocas Atoll was observed between the leeward and windward reefs, which paralleled the largest changes in sediment properties and faunal structure inside intertidal reef pools. Sediments from the tidal pools located in the windward side of the atoll were significantly finer, the organic content higher and the benthic fauna more abundant and diverse. The results of this study suggest that significant changes in the sediment properties and benthic community structure between the intertidal reef-flat pools of Rocas Atoll may be primarily conditioned by different patterns in reef growth.