Lowe's scientific endeavors were cut short by the onset of the American Civil War, for which he offered his services performing aerial reconnaissance on the Confederate troops for the Union Army. In July 1861 Lowe was appointed Chief Aeronaut of the Union Army Balloon Corps by President Abraham Lincoln. Though his work was generally successful, it was not fully appreciated by all members of the military, and disputes over his operations and pay scale forced him to resign in 1863. Lowe returned to the private sector and continued his scientific exploration of hydrogen gas manufacturing. He invented the water gas process by which large amounts of hydrogen gas could be produced from steam and coke. His inventions and patents on this process and ice making machines made him a millionaire.