Phelps served on the Labrador Coast and then with the Mediterranean Squadron from March 1840 to September 1843. He then served aboard the sloop in the Brazil Squadron. He was assigned to the United States Naval Academy in October 1843 and graduated in February 1846. He rejoined Boston for duty as a member of the Gulf Squadron from October 1846 through February 1847, and then served aboard the from February to May 1847. After duty aboard the, the flagship of the Mediterranean Squadron from June 1849 through December 1850, he transferred to the and served in the Mediterranean Squadron from December 1850 to February 1851. He then served in the Coast Survey from May 1851 until August 1852. He served in the Indian War in Washington Territory. While serving on the, he was active at the Battle of Seattle which took place on 26 January 1856. In 1882, he wrote Reminiscences of Seattle: Washington Territory and the U. S. Sloop-of-War "Decatur" During the Indian War of 1855–56
When the American Civil War began, Confederate forces destroyed or sabotaged many navigational aids in the Potomac River. Phelps was called on to use his experience conducting coastal surveys to chart the Potomac River. He was part of the expedition sent to relieve Fort Sumter and assisted in secretly surveying and marking the Confederate coast. He later conducted a secret survey of Virginia coastal waters and was recognized by the Secretary of the Navy for his efforts. In September 1861, he was transferred to command the steamer and surveyed and buoyed Hatteras Inlet in preparation for Union incursions into the inlets and rivers, along with other coastal inlets. His ship engaged the Confederate gunboat in Hatteras Inlet on 14 November 1861, and skirmished with gunboats in Pamlico Sound. He engaged the Yorktown and Gloucester Pointbatteries, sunk two Confederate vessels, and prevented Confederate forces from destroying White House Bridge during April and May 1862. Phelps was promoted to lieutenant commander in July 1862 and was charged with surveying and charting coastal waters for blockades and navigational purposes. He commanded the sloop during the successful attack on Fort Fisher, which had been protecting blockade runners' vital access to the Confederate port at Wilmington, North Carolina until it was captured by the Union on 15 January 1865. This was the last supply route open to Robert E. Lee's Army of Northern Virginia. During the Battle of West Point on April 16, 1865 in West Point, Georgia, he prevented a large force of Confederate forces from joining with their main army. In 1865, he was commissioned commander, promoted to captain in 1871, to commodore in 1879, and rear admiral in 1884, and retired in 1885.
Personal life
On January 25, 1848, Phelps was married to Margaret Riché Levy in Lake Drummond, North Carolina. Together, they were the parents of one son and two daughters:
Thomas Stowell Phelps, Jr., who also attained the rank of Rear Admiral.