In 1861–62 Kimberly served aboard the frigate in the West Gulf Blockading Squadron, taking part in the Mississippi River operations at Port Hudson, Grand Gulf, and Vicksburg, and receiving promotion to lieutenant commander on July 16, 1862. In 1863–64 he served as the executive officer of the steam sloop , seeing action at the Battle of Mobile Bay, after which he was warmly commended for his gallant and efficient service. After the war, he joined the Military Order of the Loyal Legion of the United States.