USS Winnebago was one of four monitors employed by Rear Admiral David Glasgow Farragut in the Battle of Mobile Bay. Their mission was to facilitate the entry of his squadron into the bay by bombarding Fort Morgan, which controlled the bay's entrance, and engaging the Confederate ironclad Tennessee if she tried to interfere. Winnebago was the third ship in the line of monitors. Though her turrets were frozen in train by broken mechanisms, her crew had man-handled them around to the starboard broadside, and she was able help in suppressing Fort Morgan's resistance with shot and shell, and with a shroud of dense gunsmoke that largely concealed the Union ships as they steamed past.

During the engagement with CSS Tennessee shortly after Farragut's ships had entered Mobile Bay, Winnebago played a supporting role. Since her turret troubles prevented her from engaging closely, she remained at a moderate distance from the enemy ship, training her guns on it by maneuvering her own hull and firing as the guns came on target.