Due to the far-reaching impacts of human influence, marine protection is no longer about preserving intact environments, but restoring degraded ones. What is not clear is where we should be protecting to maximise restoration efforts, particularly in coastal soft sediment environments given their heterogenous nature. This research uses ecological approaches to assess the state of environment, and to determine the potential for restoration, in the absence of baseline data. This is a case study of the benthic communities at Te Hauturu-o-toi (Hauturu), an area that has had commercial and recreational scallop dredging. Initial sampling of macrofauna across the region was undertaken and various statistical approaches including traits analysis and beta diversity have been applied. The results of this research have demonstrated that connectivity exists between sites, with particular areas being more important for contributing to overall biodiversity. There are particular species that play key roles in structuring the environment, and performing important functions. We cannot use a lack of baseline data as an excuse any longer, and this case study provides an approach to making meaningful marine conservation decisions that will result in ecosystem restoration.