This report presents the results of seabed mapping and habitat classification surveys completed in Darwin Harbour during 2011 and 2013 as part of the Northern Territory Government's marine habitat mapping program. This research aims to provide baseline data on the existing marine habitats and characteristics of the Darwin Harbour region. It is a collaboration between Geoscience Australia (GA), the Australian Institute of Marine Science (AIMS), the Department of Land Resource Management (DLRM) and the Darwin Port Corporation. Key objectives are to: - Produce detailed maps of the bathymetry and derived parameters such as slope and rugosity, - Classify the seabed into areas of hard and soft substrate, and, - Produce seabed habitat maps (or seascapes). Data collection was completed in two stages comprising a multibeam survey, undertaken on the MV Matthew Flinders in 2011 by DLRMs predecessor, the Department of Natural Resources, Environment, the Arts and Sport (NRETAS), GA, AIMS and the Darwin Port Corporation; and, a seabed sampling survey undertaken in 2013 on the MV John Hickman, by DLRM and GA. Data acquired from the surveys included continuous high-resolution multibeam sonar bathymetry and acoustic backscatter, video and still camera observations of seabed habitats and biological communities, and physical samples of seabed sediments. Key outcomes from the surveys include: 1. Improved understanding of the seabed of Darwin Harbour. The main seabed geomorphic features identified in Darwin Harbour include banks, ridges, plains and scarps, and a deep central channel that divides into smaller and shallower channels. Acoustically hard substrates are found mostly on banks and are associated with rocky reef and sponge gardens, and are often overlain by a thin veneer of sandy sediment. In contrast, plains and channels are characterised by acoustically soft substrates and are associated with fine sediments (mud and sand). 2. Classification of physical seabed properties to produce a Seascape Map for Darwin Harbour. Six seascape classes (potential habitats) were derived using an Iterative Self Organising (ISO) unsupervised classification scheme. These six classes are related to statistically unique combinations of seabed substrate, relief, bedform and presence of sediment veneer (quite often inferred from presence of epibenthic biota). The results presented in this report demonstrate the utility of multibeam acoustic data to broadly and objectively characterise the seabed to describe the spatial distribution of key benthic habitats. This is particularly important technique in high-turbidity settings such as Darwin Harbour where the application of satellite and aerial remote sensing techniques can be limited. The results of this study will be used for the planning and analysis of data from upcoming benthic biodiversity studies as they: - Provide robust near-continuous physical variables that can be used to predictive modelling of biodiversity; - Provide high-resolution coverage of near-continuous variables that describe the key physical characteristic of the seabed of the harbour, and; - Enhance survey sample design by providing indicative locations of likely similar biology communities.