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Replacing natural habitats with artificial structures such as pier-pilings, jetties, and seawalls has important consequences to abundances of biota. It is, however, not often known whether these are direct (the novel habitat alters abundances of some species) or indirect (the novel habitat directly alters some aspect of the behavior or ecology of some species, which, in turn, alter abundances of other species). Marine animals in some modified habitats in Sydney Harbour provide experimental opportunities to test hypotheses to distinguish between direct and indirect processes. Covers of bryozoans and hydroids were greater on kelp growing on pilings than on kelp growing on natural reefs. The epifauna may be affected directly by the pilings or indirectly, i.e., the structure affects characteristics of the kelp which, in turn, influence covers of epifauna. Thus, differences in covers of epifauna on kelp can be due to: (1) factors associated with the primary habitats (pilings vs. reefs), (2) differences between characteristics of the kelp found in each habitat, or (3) an interaction between these factors (habitat and/or type of kelp). Kelp were experimentally transplanted between pilings and reefs, demonstrating that properties of the habitat directly affected covers of epifauna, which were not influenced by the type of kelp that grows on pilings or rocky reefs. Manipulative experiments to unconfound multiple components of habitats influencing disturbances to biota are needed to understand human impacts on natural systems.