She got underway again on March 17 but returned to Hampton Roads for repairs when her port propeller became fouled in a buoy anchor line.

It looked a little like this [reasonably accurate sketch in letter] but of course I am not an artist..."[4] As the day of attack on Charleston approached, Keokuk and USS Bibb were busy laying buoys to guide Rear Admiral Samuel Francis Du Pont's ironclad flotilla, which included USS New Ironsides, seven monitors (Weehawken, Passaic, Montauk, Patapsco, Catskill, Nantucket, and Nahant), and Keokuk, into the strongly fortified Confederate harbor.

The Union ships crossed the Stono Bar on April 6 but were prevented from attacking that day by hazy weather which obscured targets and blinded pilots.

The First Battle of Charleston Harbor began at noon on April 7, but difficulties in clearing torpedoes from the path of Du Pont's ironclads slowed their progress.

Southern obstructions and a strong flood tide made the ironclads virtually unmanageable, while accurate fire from the forts played upon them at will.

This brought her less than 600 yards (550 m) from Fort Sumter, where she remained for half an hour receiving the undivided attention of the Confederate cannons.

Her crew kept her afloat through the night, but when a breeze came up on the morning of April 8, 1863, Keokuk began taking on more water, filled rapidly, and sank off Morris Island.

To avoid attracting the attention of Union forces, work was done at night, during low tide, with the Confederate ironclads Palmetto State and Chicora providing protection.

The other gun tube can still be seen on the Charleston waterfront at White Point Garden, mounted on an incorrect iron fortress carriage.