[2][3] Robert J. Walker's first operations involved surveying the waters of Mobile Bay in 1848, and her first commanding officer, Carlile P. Patterson, reported that year on her performance and capabilities compared with those of sailing ships.

Early on the morning of 21 June 1860, Robert J. Walker had completed her most recent hydrographic survey work and was bound from Norfolk, Virginia, to New York City in rough seas with a crew of 72 and the wife of the executive officer on board.

[2][4] She sank in less than 30 minutes in the Atlantic Ocean off the coast of New Jersey approximately 12 nautical miles (22 km; 14 mi) southeast of Absecon Inlet Light, with a loss of 20 men.

[3] With the American Civil War approaching, no inquiry into the cause of the Robert J. Walker disaster ever took place, and the Coast Survey did not pursue the matter of Fanny's presumed culpability in the sinking.

[3] A commercial fisherman found the wreck of Robert J. Walker in the 1970s, 10 nautical miles (19 km; 12 mi) off the New Jersey coast in 85 feet (26 m) of water, and divers visited it regularly thereafter, but it remained unidentified until 2013, when NOAA announced that a positive identification had been made.