Returning to New York during November 1862, she was decommissioned for repairs, and was recommissioned 7 March 1863 for service with the North Atlantic Blockading Squadron.

She was particularly successful in this assignment, capturing a steamer and a schooner off Wilmington, North Carolina, in June 1863, and aiding the destruction of a number of British steamers used as blockade runners in February 1864, including PS Fanny and Jennie.

Again out of commission for repairs between 12 December 1864 and 26 February 1865, Florida sailed 10 March with supplies for ships on station along the Atlantic coast.

She proceeded through the Gulf of Mexico to New Orleans where she embarked Confederate prisoners from the ram CSS Webb, transporting them to New York.

On her final voyage, Florida sailed in the West Indies from 4 January 1866 to 8 April 1867.