In March 1861, Rodgers was in the service of the U.S. Navy. At the outbreak of the war, his first assignment was to be to remove U.S. naval vessels and assets from the navy yard at Norfolk. He was captured by the Virginia state militia, but since Virginia had not yet joined the Confederacy, he was returned to Washington. Next, he was made responsible for the organization of the Western Flotilla before he assumed command of the James River Flotilla. In 1862, he supported the Union Army of the Potomac during the Peninsula campaign. In May 1862, he led an independent expedition, which attacked at Drewry's Bluff, however, he was forced to turn his force back down the river. In July, he received a promotion to captain, and a transfer of command to an ironclad, the Weehawken. In May 1863, he participated in the renewed effort to take Fort Sumter. His actions earned him a promotion to Commodore. This was his last active service in the course of the war.
