Biogenic structures that persist post‐mortem are ubiquitous, but rarely considered as key ecological features. Post‐mortem structures in many ecological systems exert community‐level effects and thus the dynamics of their degradation (i.e. taphonomy) become important in affecting community functions and ecosystem services, and these often‐overlooked effects may rival the influence of recruitment and typical post‐recruitment processes. Moreover, in some highly researched habitat types, post‐mortem structures may be mistaken for living organisms, thus introducing significant error into our understanding of population processes. We examined widespread patterns and processes in marine assemblages with calcareous tubeworms and brackish‐water assemblages with bryozoans, in order to test the importance of taphonomy for populations and communities. In tubeworm assemblages, taphonomic variability caused differential accumulation of post‐mortem structures, exerting community‐level influence, and importantly it negated effects from recruitment on the community functions. For tubeworms and bryozoans, proportions of post‐mortem structures varied between sheltered and exposed habitats with overall distributional variability being caused by the share of post‐mortem structures, not living animals. Population‐level inferences in such systems would be extremely problematic without careful differentiation of dead/living structures. Dynamics emerging from the interaction of taphonomic processes and recruitment ecology are relevant for many other important biogenic habitats, especially coral reefs with death assemblages of bleached corals; a failure to consider variability in processes acting on the death assemblages, alongside the living, may severely distort understanding of patterns and processes in populations and communities.