A multi-beam sonar (MBS) has been used to map Australia’s continental margin seabed from the marine national facility vessel Southern Surveyor on opportunistic transit and research voyages since 2004 with 0.35 M km2 mapped. The MBS data are used to infer key ecological features based on bathymetry (e.g. seamounts, canyons, terraces, banks and deep reefs) and backscatter data for ecological hard (consolidated, e.g. rock for attachment of fauna) and soft (unconsolidated, e.g. mud for burrowing fauna) substrate. Seabed consolidation inference is consistent with a seabed scattering model. To consistently infer ecological significant hard and soft substrate from the backscatter data requires minimisation of errors due to changing absorption (~2 dB) with temperature and depth, calibration drift, changes in pulse length and estimates of area insonified due to seabed slope (<8 dB). Area insonified corrections were required for both across and along-ship slopes. Highest corrections were needed for along-ship slopes in canyon regions and large incidence angles (>60°). A data collection and processing framework is described that works towards a national backscatter mapping program for environmental seabed mapping. Data collected and automated processing for depth, sound absorption and area insonified at level 2 of a possible 5 level data processing hierarchy is available for viewing at http://www.marine.csiro.au/geoserver.