Geoscience Australia (GA), the Australian Institute of Marine Science (AIMS) and the Department of Environment and Natural Resources within the Northern Territory Government (DENR) undertook collaborative seabed mapping surveys in the Darwin-Bynoe Harbour region between 2015 and 2018. This seabed mapping project forms a core component of a four-year collaborative research program to improve knowledge of the marine environments in the Darwin and Bynoe Harbour regions through the collation and acquisition of baseline data that enable the creation of habitat maps to better inform marine resource management decisions. Mapping and sampling in the survey area utilised multibeam echosounders, sub-bottom profilers, underwater cameras and grab samplers. In total, this data package extends over an area of 1978 km2, including 1754 km2 mapped using multibeam echosounders, during four marine surveys over 247 days. The baseline environmental data acquired in this program provides new insights into the marine environments of the Greater Darwin and Bynoe Harbour region, will inform future environmental assessments in the region and help build our knowledge of seabed features and processes in tropical northern Australia.