Skeletal concentrations, defined here as deposits ≥ 10% by volume invertebrate bioclasts (> 2 mm), are very common targets of paleobiological investigations. The complex interactions among biological, taphonomic, and physical environmental processes influence the type and quality of information that can be drawn from these paleobiological repositories. This study examines the relative roles of bioclast input and burial on the formation of Middle–Upper Devonian skeletal concentrations from tropical carbonate-dominated settings. Based on original field observations of skeletal concentrations and host lithologies, skeletal concentrations are compared (1) between a thermally subsiding passive margin (Nevada) and a relatively stable cratonic interior (Iowa) and (2) across a range of comparable subtidal depositional environments. The majority of skeletal concentrations are thin (≤ 30 cm), monotypic, have simple internal stratigraphy, and exhibit moderate to high degrees of skeletal fragmentation and disarticulation. Compared to the subsiding margin of Nevada, the cratonic interior of Iowa preserves a higher proportion of polytaxic skeletal concentrations with complex internal stratigraphy and higher taphonomic damage, consistent with control by delayed or slow burial. From shallow to deep subtidal environments, stratigraphic thickness and internal complexity decrease and fragmentation increases, consistent with strong control of these attributes by the frequency of physical and biogenic reworking. While low bioclast production rates may exert a dominant control on the failure to accumulate thick, dense skeletal concentrations in these deposits, taphonomic and physical environmental processes, such as low net sediment accumulation, sediment winnowing and starvation, and bioturbation can explain much of the variation in Middle–Upper Devonian skeletal concentrations.