Before dawn 28 June, Porter's ships opened fire on the Confederate fortress and shelled the southern batteries while Farragut dashed by the river stronghold.

On 24 July, en route to Baltimore, Maryland, for repairs, she captured Tubal Cain east of Savannah, Georgia, as the British blockade running steamer tried to slip into Charleston, South Carolina, with munitions.

From November to March 1864, she assisted in the blockade of Mobile, Alabama, bombarding Fort Powell at the entrance to Mississippi Sound 16–29 February.

On 5 August Octorara participated in the Battle of Mobile Bay, passing Fort Morgan lashed to Brooklyn.

She continued to operate in the vicinity of Mobile until July 1865, firing on fortifications and taking part in the capture of the city 12 April 1865.