In addition to her tugboat duties, she was used by the Navy as a gunboat to patrol and blockade navigable waterways of the Confederacy to prevent the South from trading with other countries.

On 23 November shortly after midnight, Shawsheen and USS John L. Lockwood bombarded a Confederate camp above Newport News on the Yorktown Road.

On 2 January 1862, Shawsheen was ordered to Hatteras Inlet, North Carolina, where a task force was assembling to attempt to capture Roanoke Island, the key to Albemarle Sound.

By the end of the next day, the conquest of the island was complete providing the Union Navy with a base which proved invaluable throughout the remainder of the war.

On the night of 13 and 14 March 1863, Shawsheen, with Hunchback, Hetzel, and Ceres, beat off a surprise attack on Fort Anderson on the Nuese River.

On 26 May, Shawsheen joined Ceres and USS Henry Brinker in an expedition up the Nuese during which they captured a number of small schooners and boats.

Perhaps her most productive day came on 20 July when she took five schooners—Sally, Helen Jane, Elizabeth, Dolphin and James Brice—near Cedar Island, in the Nuese River.

On 1 May 1864, she and USS General Putnam operated in the Pamunkey River protecting Union troops who had earlier in the day occupied West Point, Virginia.