Immediately after commissioning, Hydrographer steamed to Newfoundland, where she spent the remainder of 1942 charting the approaches and harbor to the important Allied base at Argentia.

She returned to the Norfolk Navy Yard 7 November 1942; and, after alterations to fit her for duty in the Pacific, sailed 30 December for San Diego, via the Canal Zone.

As the fleet continued to press toward Japan in a series of amphibious landings, Hydrographer sailed from Guam 1 October bound for the Palaus.

In the months that followed, the ship charted and surveyed many islands in the southern Palaus, helped to establish anchorages and seaplane landing areas, and buoyed channels.

Getting underway again 16 August 1945, she made further surveys at Eniwetok, Wake Island, and Kwajalein before sailing from Pearl Harbor for the United States 3 January 1946.