The naval base was opened in 1932 as HMAS Penguin IV and on 1 August 1940 it was renamed as HMAS Brisbane. The base was again renamed HMAS Moreton in 1942. The base was located at the corner of Merthyr Road and Gray Street, in New Farm, Brisbane and had its own wharves, warehouse buildings and assembly areas.
Post Vietnam the base was home to the Royal Australian Navy's amphibious forces including HMAS Tobruk and the Balikpapan class landing craft. For much of this time much of the army's amphibious capacity was based locally. Gallipoli Barracks based 6th Battalion, Royal Australian Regiment was Australia's lead amphibious assault unit whilst 35 Water Transport Squadron was based at Bulimba Barracks, Brisbane, Queensland with LCM.
HMAS Moreton was decommissioned in 1994 and many of its services relocated to Bulimba Barracks under the authority of Naval Headquarters Southern Queensland. Naval amphibious forces are currently based at HMAS Kuttabul.
The site of the former base has been transformed into residential apartments. Two historic buildings associated with the base, the Commonwealth Acetate of Lime Factory and Amity, are listed on the Queensland Heritage Register.