This dataset contains multibeam sonar bathymetry data from seabed mapping surveys on the Van Diemen Rise in the eastern Joseph Bonaparte Gulf of the Timor Sea. The survey was conducted under a Memorandum of Understanding between Geoscience Australia (GA) and the Australian Institute of Marine Science (AIMS) in two consecutive years 2009 (GA survey number GA-0322 and AIMS survey number SOL4934) and 2010 (GA survey number GA-0325 and AIMS survey number SOL5117). The surveys obtained detailed geological (sedimentological, geochemical, geophysical) and biological data (macro-benthic and infaunal diversity, community structure) for the banks, channels and plains to investigate relationships between the physical environment and associated biota for biodiversity prediction. The surveys also provide Arafura-Timor Sea, and wider northern Australian marine region context for the benthic biodiversity of the Van Diemen Rise. Four study areas were investigated across the outer to inner shelf. Refer to the GA record 'Methodologies for seabed substrate characterisation using multibeam bathymetry, backscatter, and video data: A case study for the Eastern Joseph Bonaparte Gulf, Northern Australia' for further information on processing techniques applied (GeoCat: 74092; GA Record: 2013/11).