Mattabesett departed New York on April 21, 1864 for duty in the North Atlantic Blockading Squadron and arrived at Hampton Roads on April 23 as escort to USS Onondaga. Continuing down the coast to enter the North Carolina Sounds, she took part in an engagement between Union forces and the Confederate ram CSS Albemarle, accompanied by CSS Bombshell and CSS Cotton Plant, off the mouth of the Roanoke River on May 5. In the course of the battle, leading to the capture of Plymouth, North Carolina by Confederate forces, Mattabesett, with USS Sassacus, captured Bombshell, but Albemarle and Cotton Plant escaped.