After repairs, Weehawken proceeded to Wassaw Sound, Georgia, on 10 June to block the expected sortie of ironclad CSS Atlanta.

Weehawken and Nahant weighed anchor to meet Atlanta which ran hard aground only moments after entering the sound.

With only five shots, Rodgers blew the roof off Atlanta's pilothouse and pierced the grounded ram's casemate, putting two gun crews out of action.

Rodgers became a national hero and received commendations from Secretary of the Navy Gideon Welles, President Abraham Lincoln, and Congress.

On 10–11 July, Union ironclads Catskill, Montauk, Nahant, and Weehawken shelled Confederate batteries at Fort Wagner on Morris Island, South Carolina, to cover an Army amphibious landing under Brigadier General Quincy A. Gillmore.

Despite additional bombardments on 18 and 24 July, the monitors failed to silence the fort, leaving General Gillmore's troops pinned down on the beach caught between a murderous hail of cross fire.

Weehawken, Montauk, Nahant, Passaic, and Patapsco now took aim at Fort Sumter, pounding it to rubble during two separate bombardments on 23 August and 1–2 September.

Admiral Dahlgren demanded Sumter's surrender on 7 September and ordered Weehawken to deploy in a narrow channel between the fort and Cumming's Point on Morris Island.