This study evaluates encrustation and bioerosion of brachiopods (Bouchardia rosea) and bivalves (Semele casali) occurring on the inner shelf of the Southeast Brazilian Bight, accounting for differences in water depth, sediment type, host size, and time averaging. Frequencies of colonization covary across sites, but brachiopods are more frequently encrusted than bivalves at all sites, although this difference may disappear after standardization for shell size, depending on the chosen metric. Size selectivity during sclerobiont colonization appears to change as a function of their population density, rather than substrate differences between hosts. Sediment grain size and composition do not appear to exert environmental controls on encrustation or bioerosion, nor does either vary as a function of water depth alone. Radiocarbon-calibrated aspartic acid racemization dating of individual host valves shows similar age ranges and age structures for both hosts. Both epifaunal brachiopods and infaunal bivalves are colonized rapidly, within years to decades, with no further increase over millennial timescales. Rapid burial and sequestration from sclerobiont larvae is inconsistent with rapid postmortem exhumation and encrustation of infaunal bivalves, and indicates a brief temporal window for colonization. The relative abundance of sclerobionts is volatile over the time interval represented by dated valves, but temporal stability is seen in presence-absence data for epibiont and endobiont taxa. These results support the utility of taphonomic deployment experiments for investigating long-term patterns of hard-substrate colonization, but indicate careful consideration of host size is required for comparison of sclerobiont assemblages within or among taxa.