Gunboat Winona was part of the Western Gunboat Fleet assembled by Navy Flag Officers COM. John Rodgers and RADM. Andrew H.
Foote under the jurisdiction of the War Department. The fleet was based at Cairo, IL for operations on the western waters. The fleet
consisted of all the warships operating on the Ohio, Mississippi and Red Rivers and their tributaries.

The fleet was renamed the Mississippi River Squadron and transferred to the Navy Department in 1862 because the Army had been interfering with naval operations in the inland waterways.
The Winona served at first at the mouth of the Mississippi River. Thereafter, she served in the siege of Vicksburg, then on the Yazoo
River, and eventually in Mobil Bay. After the fall of Mobile, the Winona resumed duty on the Mississippi River.