The Maritime Archaeology department, based in the WA Shipwrecks Museum, primarily researches shipwreck archaeology from the Western Australian coast. Its staff members are involved in developing artefact management and cataloguing strategies, outreach and wreck-access programs, site-inspection techniques, and studies of diverse maritime sites, such as iron ship archaeology and underwater aviation archaeology.

The collection and conservation of archaeological material recovered from historic shipwrecks found along the Western Australian coast led to the establishment of the WA Shipwrecks Museum, one of the few museums in the world with a specific focus on the preservation and display of maritime archaeological material.

The collection comprises material dating from the early seventeenth century to the late nineteenth century. It provides tangible evidence of the early presence of English, Portuguese, Dutch and American seafarers on the west coast of Australia.

The best-known shipwrecks of this early presence are Trial (1622), Batavia (1629), Vergulde Draeck (1656), Zuytdorp (1712), Zeewijk (1727), Rapid (1811), and Correio da Azia (1816). Furthermore, it has an important research collection relating to the shipping activity associated with British colonisation of Western Australia and to the development of the State, such as the ex slave-ship James Matthews wrecked in 1841, the iron barque Sepia in 1898, and the SS Xantho in 1872.