On 5 November 1861, Seneca and three other Federal Union gunboats engaged and dispersed a Confederate squadron near Port Royal, South Carolina; two days later, she took part in the capture of Port Royal, which proved to be an invaluable Union naval base throughout the remainder of the Civil War.
She was recommissioned on 3 October, Commander George Belknap in command, and was assigned to the North Atlantic Blockading Squadron.