After acquiring her from the United States Navy, the Coast Survey commissioned Phoenix in 1845 and operated her in its Atlantic fleet throughout her career.

[2] A tornado struck Phoenix while she rode at anchor in Mississippi Sound on the U.S. Gulf Coast on the night of 31 March 1854, causing her to capsize and sink in 20 seconds.

The crew managed to free one of her boats about an hour after she sank and row to shore safely.

[2] Phoenix spent the 1855 field season transporting and housing Coast Survey teams who triangulated an approximately 60-mile (97-kilometer) stretch of coast between Pascagoula, Mississippi, and the entrance to Lake Pontchartrain in Louisiana.

In 1856, she supported survey parties along the coast of Texas, arriving there with significant storm damage after a rough passage.