Previously, she had been in commission in the United States Coast and Geodetic Survey from 1963 to 1970 as USC&GS Whiting (CSS 29).

In 1989 she underwent a major upgrade involving the installation of Hydrochart II, which employed a Microvax computer system to acquire and process hydrographic data.

[7] After receiving word that the Piper Saratoga II HP flown by John F. Kennedy, Jr. had disappeared during a flight on the evening of 16 July 1999 and was feared to have crashed in the Atlantic Ocean off Martha's Vineyard, Massachusetts, Whiting, under the command of Lieutenant Commander Gerd F. Glang, interrupted her survey operations in the Delaware Bay on 18 July to make a 24-hour voyage at about 12 knots (14 mph; 22 km/h) to the search area and participate in the search for the aircraft and its passengers.

Later on 21 July, the two ships were released from duty in the crash area, and Whiting set course for Washington, D.C., to take part in the assumption-of-command ceremony for incoming NOAA Corps Director Rear Admiral Evelyn J.

The U.S. Coast Guard requested her support in the search for the downed aircraft, and she soon got underway for Naval Station Newport, Rhode Island, where she replenished her supplies and refueled before proceeding to the crash area.

After only a day of search operations, however, a gale with 50-knot (58-mph; 93-km/h) winds and 20-foot (6.1-meter) seas forced Whiting and U.S. Navy survey ships in the area to return early on 3 November to Newport, where Whiting's crew compared their survey data with data collected by U.S. Navy ships.

[14] A break in the weather allowed Whiting to return on 5 November to continue her bottom-mapping operations; although she had to suspend mapping operations briefly when the towfish containing her sidescan sonar became entangled in a lobster pot and was damaged, her crew was able to improvise a night repair in difficult weather conditions and put the sonar back into service.

[15] Whiting's bottom map combined with charts provided by NOAA's Office of Coast Survey allowed the U.S. Navy rescue and salvage ship USS Grapple (ARS-53) to anchor safely over the debris field without disturbing the wreckage.

[9][16][17][18][19] In July 2001, NOAA's Office of Ocean Exploration asked Whiting to search for the wreck of the U.S. Navy submarine USS S-5 (SS-110), which sank 15 nautical miles (28 kilometres) off Cape May, New Jersey, in September 1920.

Whiting, which had just completed a summer in port at Norfolk, Virginia, and was bound for Boston, Massachusetts, to conduct hydrographic survey operations in New England, paused off Cape May in late July 2001 to search for the wreck.

Accordingly, by the authority of the United States Secretary of Commerce, Whiting was transferred to Mexico in a ceremony at Norfolk, Virginia, on 28 April 2005.