New Orleans operations

The schooner was assigned to Commander David Dixon Porter's mortar flotilla and proceeded to Ship Island, Mississippi to support Flag Officer David Farragut's attack on New Orleans, Louisiana. The mortar schooners shelled the Southern riverside forts for a week before Farragut's deep draft ships raced past the Confederate batteries and captured New Orleans, Louisiana.

Mississippi River operations

The schooners sailed to the entrance to Mobile Bay which they blockaded until Flag Officer Farragut called them back to the Mississippi River to bombard new and increasingly strong Confederate batteries at Vicksburg. They shelled the Southern emplacements at that river fortress during Farragut's dash past Vicksburg to meet Flag Officer Davis's Western Flotilla.

While Farragut was above the forts awaiting troops for a joint Army-Navy attack on Vicksburg, the collapse of General George B. McClellan's peninsula thrust toward Richmond caused the Secretary of the Navy to recall Porter and twelve of his schooners for duty supporting Union Army operations in the Richmond/Washington theater. However, Sarah Bruen was one of the mortar schooners left on the Mississippi River. She remained in the West Gulf Blockading Squadron until ordered north in the spring of 1864.

Ordered to the East Coast

After repairs at New York, she was ordered to Port Royal, South Carolina, on 27 June 1864. The remainder of her active service in the Civil War was performed on blockade duty inside Charleston Harbor's bar.