On 17 July 1862, the double-ender sailed for the West Indies for operations against Confederate blockade runners and raiders on the high seas. The success of Confederate cruisers, especially and , in operations against Union shipping prompted the Department of the Navy on 8 September 1862 to put Commodore Charles Wilkes in command of a "flying" West India Squadron created specifically to seek out and destroy the Confederate raiders. "Sonoma" was assigned to this squadron. While "Sonoma" never engaged "Florida" or "Alabama", she did operate successfully against blockade runners.