Hendrick Hudson was captured by while attempting to run the blockade at St. Andrews Bay, Florida on 6 April 1862. She was taken to Philadelphia, Pennsylvania for adjudication, where she was condemned and purchased by the United States Department of the Navy from the prize court on 20 September 1862. Renamed Hendrick Hudson, she commissioned 30 December 1862 at Philadelphia, Acting Master John E. Giddings commanding.
Assigned to the East Gulf Blockade
Assigned to the East Gulf Blockading Squadron, Hendrick Hudson sailed to Hampton Roads, Virginia, arriving 3 January 1863, and from there proceeded to her blockading station off East Pass, St. George's Sound, Florida. On station 1 February, Hendrick Hudson began her long months of arduous blockade duty, working to shut off commerce through the multitude of small inlets and passes of the Florida coast.
Capturing blockade runners
She remained off St. George's Sound until late August 1863, capturing schoonerMargaret on 1 February and schooner Teresa on 16 April. She then retired to Boston, Massachusetts for repairs and refitting, returning to a new station off the mouth of the Suwannee River on 28 December. Resuming her blockading duties, Hendrick Hudson encountered a small schooner off Key West, Florida on 21 March 1864 and stood toward her. The blockade runner, Wild Pigeon, suddenly turned across Hendrick Hudson's bow, however, and was inadvertently rammed and sunk. None of her assorted cargo could be recovered.
The steamer continued her blockading duties through 1864, spending much of her time in busy Tampa Bay and St. Marks, Florida. A group of her men went ashore on an expedition on 12 November and engaged some Confederate soldiers briefly, in one of the many forays ashore by personnel of the East Gulf Squadron.
Hendrick Hudson participated 27 February to 7 March 1865 in an expedition with Union Army units in the vicinity of St. Marks, Florida. The steamer helped blockade the river and some of her crew went ashore with the Army in an attempt to capture Confederate positions in what came to be known as the Battle of Natural Bridge. Two of the ship's sailors were awarded the Medal of Honor for their part in this battle: Seaman John Mack and Coxswain George Schutt.
Post-war decommissioning and subsequent career
Following the end of the U.S. Civil War, Hendrick Hudson was not retained in the squadron, and was ordered north 15 July 1865. She decommissioned 8 August 1865 at Philadelphia and was sold on 12 September. The ship was subsequently redocumented SS Hendrick Hudson and operated in commercial service until she was lost near Havana, Cuba on 13 November 1867.