After a successful career as a blockade runner, she was captured by USS Iroquois off the coast of Cape Fear River, North Carolina, 24 July 1863.

Upon arriving New York, she debarked her sick sailors at quarantine, and got underway for a cruise in the northwest Atlantic as far as St. John's, Newfoundland.

Underway for Key West the next day, Merrimac ran into still worse weather which she fought until turning north on the 14th to seek the first port.

On the afternoon of 15 February 1865, Acting Master William Earle ordered the crew to abandon ship after its tiller had broken, two boilers given out and the pumps failed to slow the rising water.

That night, when the crew had been rescued by mail steamer Morning Star, Merrimac was settling rapidly as she disappeared from sight.