An accurate understanding of global patterns through geologic time depends upon multi-scale analyses of spatial variation within narrow temporal intervals. This work investigates geochemical and paleoecological patterns in modern brachiopod faunas which may serve as analogues for ancient brachiopod assemblages. The paleoclimatic utility of delta18O in the phosphatic phase of lingulid brachiopod shells requires valve secretion in equilibrium with seawater, an assumption tested (and rejected) when analyzed at scales ranging from millimeters to kilometers. By contrast, biological encrustation of the brachiopod fauna of the Southeast Brazilian Bight shows strong sensitivity to microenvironmental conditions such as host identity, shape, and size, and may prove useful for studies of ancient planktonic productivity. Comparison of encrustation patterns on naturally occurring brachiopods and bivalves collected from the same sites, and occupying the same size range, demonstrates that the results of encrustation studies on modern bivalves cannot be directly applied to ancient brachiopods. However, careful comparisons may reveal patterns of epibiont selectivity and the impact of changes in the relative abundance of host shells through geologic time. Finally, neither epibiont abundance nor diversity increase with host age as indicated by dated brachiopod shells from the past 1000 years. These results suggest that the temporal resolution of epibiont assemblages matches their spatial resolution, and strengthen evidence for competition among encrusting taxa. By documenting geochemical and paleoecological variation within shells and across a continental shelf, this work demonstrates the importance of understanding spatial variation across all scales before interpreting trends through time.