Commissioned as a Confederate privateer on September 12, 1861, Manassas was seized soon afterwards by Flag Officer G. N. Rollins, CSN, for use in the lower Mississippi River. With Lieutenant A. F. Worley, CSN, in command she participated in Flag Officer Rollins' surprise attack on the Federal blockading squadron at Head of Passes, Mississippi River, on October 12, 1861. In the action Manassas violently rammed USS Richmond, damaging her severely below the water line. Manassas, however, suffered the loss of her prow and smokestack and had her engines temporarily thrown out of gear from the impact. She managed to retire under heavy fire from USS Preble and Richmond whose shells glanced off her armor. Two months after this engagement, Manassas was purchased for direct ownership by the Confederate Government.
Under Lieutenant Worley, Manassas joined the force of Captain John K. Mitchell, CSN, commanding Confederate naval forces in the lower Mississippi. She participated in the engagement of April 24, 1862 during which Admiral David Farragut, USN, on his way to New Orleans, ran his fleet past the Confederate forts of Fort Jackson and Fort St. Philip. In the action Manassas attempted to ram USS Pensacola, which turned in time to avoid the blow and deliver a broadside at close range. Manassas then ran into murderous fire from the whole line of the Union fleet. She then charged USS Mississippi and delivered a long glancing blow on her hull, firing her only gun as she rammed. Next she rammed USS Brooklyn, again firing her gun, and injuring her rather deeply, but not quite enough to be fatal.
After this action Manassas followed the Union fleet quietly for a while, but as she drew closer Mississippi furiously turned on her. Manassas managed to dodge the blow but was run aground. Her crew escaped as Mississippi poured her heavy broadsides on the stranded Confederate vessel. Later Manassas slipped off the bank and drifted down the river in flames, tried to save her as an Manassas exploded and immediately plunged under water.