On 5 October 1862, Sonoma chased Harriet Pinckney back into port after she had attempted to slip out of Bermuda reportedly carrying "infernal machines or torpedoes ... for destroying ships in harbor."

Highlights of this service included her capture on 8 July 1864 of Ida a sidewheel steamer which had slipped out of Sapelp Sound, Georgia, and was bound for the Bahamas laden with cotton.

In December 1864, Sonoma was part of a Union naval force that landed Union Army troops and a battalion of United States Marines at Gregorie Point near Yemassee, South Carolina, in an attempt to cut the rail line between Savannah, Georgia, and Charleston, South Carolina; they were defeated by a significantly smaller Confederate force in the Battle of Tulifinny.

Assurance of Union naval control of the waters in its path enabled Sherman's army to travel fast and light and helped to shorten the war.

On 16 and 17 February 1865, Sonoma joined in the naval support of the Union Army's attack on Bull's Bay, South Carolina, a diversionary movement in the major drive on Charleston.