The ship was built for the United States Navy as USNS Littlehales (T-AGS-52) serving as one of two new coastal hydrographic survey vessels from 1992 until transfer to NOAA in 2003 when it was named after Founding Father and third U.S. president, Thomas Jefferson.

[6] During 2001 Littlehales surveyed the harbor and approaches Dakar, Senegal and experienced petty piracy early in the morning of 14 May when the watch noticed a small boat with eight persons which sped off with subsequent discovery that six mooring lines were missing.

[7][8] Examples of operations in domestic waters include surveys from 29 October 2001 to 28 January 2002 of the area of King's Bay, Georgia and St. Marys River approaches.

An example is work involving the Deep Ocean Logging Platform with Hydrographic Instrumentation and Navigation (DOLPHIN), a diesel powered semi-submersible for surveying.

Littlehales, NOAAS Whiting (S 329) and DOLPHIN surveyed parts of the Norfolk Canyon 62 nmi (71 mi; 115 km) off Cape Charles, Virginia.

The vessel carries two aluminum survey launches equipped with multibeam swath and single-beam echo sounders and a hydrographic data acquisition system.

[15] On 6 April 2010, Thomas Jefferson departed Norfolk bound for the Gulf of Mexico to conduct a five-month-long effort to map the seafloor, searching for hazards to navigation.

[16] On 26 May 2010, Thomas Jefferson was underway on a mission to deploy United States Navy ocean monitoring instruments near the BP Deepwater Horizon oil spill.

It was the first commemoration ever held for the 20 men lost in the sinking, the largest loss of life in a single incident in the history of NOAA and its ancestor agencies.

Lacking exact locating data for the wreck, Thomas Jefferson held the ceremony in the general area where Robert J. Walker had sunk.

There the ship’s 38 officers and crew conducted multibeam echo sounder (MBES) and side scan sonar (SSS) hydrographic surveys in the island ports and bays.

Over three weeks the crew surveyed 13 areas and no fewer than 18 individual port facilities, as well as conducted emergency repairs to three tide and weather stations.