On 21 January 1862, she joined USS Ethan Allen in capturing the Olive Branch bound from Cedar Keys to Nassau, Bahamas, with a cargo of turpentine.

She again cooperated with Ethan Allen on 26 January 1862 in manning and equipping a boat expedition to the mouth of the Manatee River which captured the sloop Mary Nevis and burned Confederate cavalry barracks.

Early scurvy became a serious problem for the crew prompting Rear Admiral Lardner to order Kingfisher to Boston, Massachusetts.

The bark was stationed in St. Helena Sound, South Carolina, where she distinguished herself for efficiency in reconnaissance work and operations against small parties of Confederates ashore.

On 9 April 1863, a party from Kingfisher landed at Middleton's estate, Edisto Island, South Carolina, and captured a group of Southern cavalrymen stationed there to observe and report activity of Union ships in the area.