Now the first great conflict came on at Bull Run. Anticipating the event, Whiting was entrusted with the charge of arrangements for the moving of the army at Harper's Ferry, to the aid of Beauregard at Manassas, and had the railroad authorities kept their repeated pledges to him, reinforcements would have reached the field of Manassas in time to have crushed McDowell earlier in the day, spared much Confederate blood, and possibly cut off the retreat of the United States forces to Washington. General Whiting had in charge the blowing up of Harper's Ferry, which General Johnston pronounced a ‘masterly piece of work.’
Whiting was with the troops whose opportune arrival at Manassas saved the day, including the gallant 6th North Carolina, whose colonel (Fisher) gave up his life on the field of battle. His name is immortalized by the fortress where North Carolinians withstood the greatest bombardment that the world has ever known.
In General Joseph E. Johnston's official report of the battle of Manassas, he mentions Whiting first, of all of his staff, and declares:
Major W. H. C. Whiting, Chief Engineer, was invaluable to me for his signal ability in his profession, and for his indefatigable activity before and in the battle.
For his brilliant service on the field, President Davis, who was on the ground, wrote the following order (which I hold in my hand), entire as to text and signature:
The permanent commission was dated by the Secretary of War, August 28th, to rank from the glorious 21st July, the day of Manassas.