Commander Rodgers' first war assignment was to go with Commodore
Louis M. Goldsborough to
Gosport Navy Yard on April 20, 1861, where with other officers he was to remove Naval vessels and assets so they could not be used by the Confederates. Virginia had only just declared her secession from the Union. Upon arrival they found the yard in shambles, as
Commodore McCauley had already ordered the vessels at Gosport scuttled, including the , since he considered the yard indefensible. Commodore Goldsborough made the decision to destroy the yard, and Commander Rodgers and Army Captain of Engineers
Horatio G. Wright were given the job of destroying the drydock. They were thwarted in this attempt when the fuse was extinguished by water in the pumping gallery. Commander Rodgers and Captain Wright were captured by General
William B. Taliaferro of the
Virginia State Militia, but since Virginia had not yet joined the
Confederate States, and was therefore not at war against the United States, Governor
John Letcher returned the two officers to Washington. Commander Rodgers was then sent to the Western Rivers, where he organized the
Western Flotilla and supervised construction of the
City-class gunboats, the first ironclad
gunboats on the western rivers. He was relieved by Captain
Andrew Hull Foote, a more senior officer being required by the Navy to deal with the prickly Major General
John C. Fremont. After blockading operations off of
Savannah in command of the , he assumed command of the experimental ironclad in April 1862, operating with distinction in the
James River. He commanded the
James River Flotilla, including the USS
Galena, the ironclad , and the 90-day gunboat in an expedition up the James River in May 1862, which was stopped eight miles shy of
Richmond by Confederate fortifications at
Drewry's Bluff. The damage that the
Galena suffered in the ensuing battle caused him to report, "We demonstrated that she is not shotproof", and made him disdainful of trying experiments in the fires of war. Thereafter he supported
General McClellan's
Peninsula Campaign with Naval bombardment, preventing Confederate forces from overrunning the
Army of the Potomac's position. John Rodgers was promoted to captain July 16, 1862 and took command of the ironclad monitor . After successfully navigating her from
Brooklyn to
Charleston through the same storm that sank the , he distinguished himself during the attack on
Fort Sumter in May 1863, and in capturing the Confederate ram
Atlanta on June 17, 1863. The latter service won him the
Thanks of Congress and promotion to commodore. Unfortunately, this was his last active service in the Civil War. After recovering from an illness, he took command of the ironclad monitor . Design and construction problems with that vessel kept him occupied for the remainder of the war, though he earnestly desired a more active post. ==Post-war career==