The Ediacaran skeletal tubular putative metazoan Cloudina occurs globally in carbonate settings, which provided both lithified substrates and minimized the cost of skeletonization. Habitat and substrate preferences, and the relationship of Cloudina to other metazoans, have not been fully documented so we know little as to its ecological demands or community dynamics. In situ Cloudina from the Nama Group, Namibia (ca. 550–541 Ma) formed mutually-attached reefs composed of successive assemblages in shallow, high-energy environments, and also communities attached to either stromatolites in storm-influenced deep inner-ramp settings or thin microbial mats in lower energy habitats. Each assemblage shows statistically distinct tube diameter cohorts, but in sum Cloudina shows an exponential frequency distribution of diameter size. In reefs, we document a periodicity of size variation, where mean, minimum and maximum tube diameters vary together and show a systematic increase toward the top of each assemblage. We conclude that most Nama Group Cloudina represent one ecologically generalist taxon with highly variable size, that size was environmentally mediated, and that Cloudina could respond rapidly to periodic environmental changes. While Nama Group skeletal metazoans coexisted with soft-bodied biota, there was no apparent ecological interaction as they were segregated into lithified carbonate, and non-lithified clastic microbial mat communities, respectively. We infer that ecological flexibility allowed Cloudina to form varied communities that colonized diverse carbonate substrates under low levels of interspecific substrate competition. This is in notable contrast to the earliest Cambrian skeletal epibenthos that formed biodiverse reef communities with specialist niche occupancy.