She was one of a handful of World War II AKAs manned by officers and crew from the United States Coast Guard.

She reached Pearl Harbor on 28 October and then returned to San Diego where she reported for duty to the 5th Amphibious Force, Pacific Fleet, and was assigned to Transport Division 24.

Following a repair period lasting until 25 November, she embarked Marines and got underway for amphibious training exercises off the California coast.

She joined Task Force (TF) 53 at Pearl Harbor and sortied on 22 January for the invasion of the Marshall Islands.

She stood into the transport area off Roi and Namur Islands, Kwajalein Atoll, on 31 January and from then until 6 February, unloaded her cargo and disembarked troops.

During the remainder of February and into early March, she operated in the Solomon Islands conducting amphibious training exercises with Army troops.

On 21 March, she moved to Nouméa, New Caledonia; loaded Army personnel and equipment; and took them to Emirau Island to serve as a garrison force.

Following repairs at Espiritu Santo, Aquarius returned to Guadalcanal to conduct rehearsals with the 3d Marine Division for the projected assault on the Marianas.

After embarking Army personnel for exercises in the Humboldt Bay area, she sortied on 13 October with TG 78.1 for the invasion of Leyte.

She departed San Diego on 18 August, arrived at Guam on 4 September, and moved to Saipan three days later to load cargo and troops for use in the occupation of Japan.

She was turned over to the War Shipping Administration on 12 September, and her name was struck from the Navy list on 13 November 1946.