Restoration works are carried out to alleviate human impacts and improve habitats within ecosystems. However, human impacts may also create new (anthropogenic) habitat for species to exploit. A dilemma arises when proposed restoration works would remove anthropogenic habitat and the assemblages it supports. Sediment input into the Glenelg River has formed tributary junction plug wetlands at confluences. Sand slug removal is proposed as part of river rehabilitation, but would also drain plug wetlands. We sampled four plug wetland, four river run and three river pool sites to determine whether plug wetlands influence water quality and add to the biodiversity of macroinvertebrates in the Glenelg River. Water quality and macroinvertebrate diversity were similar in plug wetlands, river runs and river pools. Assemblages were distinct among all sites, regardless of type, so there was no characteristic ‘plug-wetland fauna’. Therefore, although removal of plug wetlands would not cause a dramatic loss of invertebrate biodiversity, it would destroy anthropogenic habitat that supports a similar range of species to natural habitats in a river subject to multiple degrading processes. Gains from rehabilitation should be weighed against the value of anthropogenic habitat and the extent of similar habitat lost elsewhere in the ecosystem.