In 1846 he was appointed acting constructor in United States Navy and superintended the building of the iron sloop-of-war USS Alleghany in Pittsburgh, Pennsylvania.
While in Pittsburgh he designed and submitted to the Navy Department plans and specifications for an ironclad warship, but his idea did not receive much attention in Washington.
He modified his previous ironclad design and submitted it to Secretary Stephen R. Mallory of the Confederate States Navy on 24 June 1861.
Chief Engineer of the Navy William P. Williamson, Lt. John Mercer Brooke and Porter developed a plan of the conversion of the scuttled and burned steam frigate USS Merrimack to an ironclad, which became CSS Virginia when commissioned in February 1862.
He was promoted to Chief Naval Constructor in January 1864 and served in that capacity to the end of the U.S. Civil War, designing many of the South's domestically-built warships.