As awareness of the extent of marine habitat degradation has grown, so too have attempts to repair them, through a combination of restoration, rehabilitation and eco-engineering. Programs targeting seagrass and seaweed restoration, and marine eco-engineering and artificial reef research have developed methodologies that successfully repair individual habitats, but have to date been uncoordinated in their efforts. Project Restore brings these programs together for the first time to address whether multi-habitat, seascape level, restoration can bring greater ecological benefit than individual habitat repair conducted in isolation. Restoration sites are being established in Sydney Harbour in which a combination of multiple types of habitat (seascape) repair are conducted together, and in which a single type of repair is being conducted alone. We expect that compared to degraded control sites, ecological benefits will be seen both at sites with either seascape or individual habitat repair. However, we also expect that recovery towards a reference (less degraded) state (as measured by metrics of ecological structure, function and connectivity) will be greater at sites with seascape versus single habitat repair. Project Restore provides a template for best practice marine seascape repair and will provide valuable insights into the ecological processes in an urbanised estuary.