This study investigated the variability of molluscan assemblages of rock pools according to location and pool size. The study was carried out in three sandstone reefs on the west coast of Ceará in northeast Brazil. The size parameters evaluated were surface area, depth, and volume of pools and pool-ocean distance. The molluscan assemblages were characterized by ecological diversity descriptors (abundance, species richness, diversity, and evenness). A total of 43 species of molluscs belonging to the classes Bivalvia, Gastropoda, and Polyplacophora were identified. The most relevant species for discriminating among the assemblies were Eulithidium affine, Cerithium atratum, Tegula viridula, and Ischnochiton striolatus. Results indicated a clear local difference in the structures of the assemblages; however, they did not differ according to the size of the pools. This indicates that sites may play a more important role in the structure of molluscan assemblages in rock pools than the association with pools.