Beginning in May through September 1864, Weitzel was assigned as chief engineer of the Army of the James, still under General Benjamin F. Butler, which was targeting the Confederate capitol, as well as its naval defenses under the remnants of the James River Squadron. He was engaged in May at Swift's Creek and the actions near Drury's Bluff and the Bermuda Hundred Campaign (against his former commander, now Confederate General P.G.T. Beauregard), and the Deep Bottom in August. By month's end, Weitzel was brevetted major general of volunteers "for meritorious and distinguished services during the civil war."