Assigned to the Gulf Blockading Squadron

Assigned to the Gulf Blockading Squadron, the schooner arrived off Fort Pickens, Florida, on 16 December 1861 and sent to Ship Island, Mississippi. She reported as a gunboat tender to the USS Colorado) at the SW Pass of the Mississippi River on 28 December. Commander T Bailey of the Colorado added a 24-pounder howitzer to her and assigned her to blockade Barataria Bay.

On 9 January 1862, she sailed to West Bay, Texas, and used her two boats to conduct a reconnaissance of the bayou there on the 10th, 11th and 12th. The shore party also destroyed some telegraph lines, as reported by Acting Master Rogers.

She then performed blockade duty off the Mississippi River passes in conjunction with the USS Colorado and was reported being there on 23 January.

Reassigned to the East Gulf Blockading Squadron

On 20 January 1862, Secretary of the Navy Gideon Welles, on splitting naval jurisdiction in the Gulf of Mexico between Flag Officers William McKean and David Farragut, assigned Samuel Rotan to the former for service in the East Gulf Blockading Squadron. However, other events would delay her reporting.

On 23 Jan 1862, she captured Confederate privateer, Calhoun, by forcing her to run aground in East Bay, formed by the Southwest-Pass and Grand-Pass fingers of the Mississippi delta. The prize had been attempting to slip into the Southwest Pass laden with over 25 tons of gunpowder, rifles, chemicals, coffee, and other assorted cargo needed by the Confederacy.

The Calhoun was pressed into Federal Service and the prize cargo and papers taken aboard the Samuel Rowan which was dispatched from Ship Island on 18 February to deliver them to the prize court in Philadelphia. Judge John Cadwalader ruled that the proceeds of the prize be shared by both the Rotan and the Colorado.^[1] The prize was deemed to be worth $16,531, and after court costs, $14,412.40 was sent to the Treasury Department, where half would be placed into the Navy Pension Fund and half would be distributed amongst the crew members of the two ships.

On March 28, she was dispatched from Philadelphia to report to Key West, Florida, under the command of Acting Master John A Rogers. As she had the prize master from the Colorado on board, she needed to rendezvous with her off the Mississippi first.

Acting Master J.D. Barclay took command on April 4. As the USS 'Colorado drew too much water to navigate the Mississippi, the Samuel Rotan was separated and dispatched to protect David Dixon Porter's mortar schooner fleet at the forthcoming Battle of Forts Jackson and St. Philip where she is pictured in a Harper's Weekly drawing of that fleet.

The schooner then joined her new squadron at Key West at the end of April. She was dispatched to blockade the Indian River on April 28 and St. Andrews Bay on May 14. Acting Volunteer Lieutenant W.W Kennison was given command on July 6 after heroic action as a gun captain when the USS Cumberland was sunk by the ironclad in Hampton Roads that previous March. (The destroyer USS Kennison was later named for him.)

Into the autumn, she blockaded the Florida coast, primarily off St. Andrews Bay and later Tampa Bay. The New York Times reported her in Key West on November 3, 1862^[2]

She sailed from Key West on 16 November for badly needed repairs in the Philadelphia Navy Yard.

North Atlantic Blockade duty

In January 1863, Samuel Rotan joined the North Atlantic Blockading Squadron and was ordered to the York River for blockade duty. Officers were Acting-Volunteer-Lieutenant, W. W. Kennison; Acting-Master's Mates, Thos. Moore, C. H. Packer and D. M. Gaskins. On February 20, she took part in the capture of the schooner General Taylor. On the morning of 24 April, she and USS Western World captured schooners, Martha Ann and A. Carson, off Horn Harbor, Virginia.

On 2 July, she took 35-ton schooner, Champion, off the mouth of the Piankatank River. On 24 July, Lt Commander Gillis reported "the blockade running in Mobjack Bay has been effectively stopped by placing the schooner Samuel Rowan at the mouth of the York River."

On the 27th, her picket boat seized a canoe which had run the blockade from the Severn River, Virginia, laden with corn, chickens, and eggs. On 10 October, her picket boat chased a yawl standing up the beach of Horn Harbor, Virginia. Its occupants jumped overboard and fled to the beach. Then the Southerners fired upon the Union sailors who came up and took possession of the little prize and its cargo of salt.

Soon thereafter, the schooner's need for repairs became serious, and she proceeded to the Norfolk Navy Yard for the work.

Late in January 1864, she was back on blockade duty off the west coast of Chesapeake Bay, and she continued this duty into the autumn. Then she was transferred to the James River to help support General U.S. Grant's operations against Richmond, Virginia, in the Petersburg Campaign. Early in December 1864, she was back off the York River and served in that area into the spring of 1865.