The overall aim of this project was to determine the geomorphological and sedimentary characteristics (biological and physical) of the Ningaloo Reef and shelf, and to identify evolutionary characteristics relevant to the maintenance of marine biodiversity. This included characterising reef growth history, coastal and seabed geomorphology, surficial sediment facies and their influence on the distribution of benthic habitats. This research presents an interdisciplinary study that provides an important baseline for future habitat mapping, biodiversity assessments, spatial planning, and fisheries management. The characterisation and mapping of benthic habitats based on physical parameters is central for the ongoing monitoring, management and conservation of the NMP’s inshore and offshore resources, particularly during a time of increasing anthropogenic and environmental pressures.