On 22 January 1862, Flambeau arrived at Port Royal, South Carolina, from which she was ordered to blockade Stono Inlet, one of the entrances to Charleston Harbor.

For the next year, she cruised off Charleston, sharing in the capture of several prizes, and sending a party ashore 28 December to destroy the abandoned fort on Bull's Island.

The following day, the Flambeau landed a rescue party, but it was intercepted and had one man killed and one wounded in the ensuing skirmish.

In February 1863, Flambeau delivered stores to ships on the coasts of Florida and Georgia, then returned to duty off Charleston until April.

After repairs at Washington, D.C., she joined her squadron at New Inlet from May through September, taking schooner Betty Kratzer prize on 23 June.