Since rumors were then circulating that Confederate ironclads were about to attempt to recapture New Orleans, Stockdale steamed down the Mississippi River to reinforce Admiral David Farragut's ships in defending that strategic city, and she served in the West Gulf Blockading Squadron through the end of the Civil War.

On the morning of the 5th, while David Farragut was leading his squadron into Mobile Bay, Stockdale steamed toward Fort Powell and bombarded that Southern fortress.

In the months that followed, Stockdale continued to serve in the West Gulf Blockading Squadron for the most part, and supported mop-up operations in and around Mobile Bay.

On the 11th, Stockdale again joined Randolph in an expedition—this time up the Fish River to seize a sawmill engine, some livestock, and 60,000 board feet (100 m3) of lumber.

On 8 December, Stockdale and USS John P. Jackson captured schooner Medora in Mississippi Sound as the blockade runner was attempting to slip to sea laden with cotton.