The 71st participated in the Peninsular Campaign of 1862, although it isn't clear whether Wistar was actually present; at the Battle of Seven Pines (May 31 and June 1) the regiment was led by its major, and during the Seven Days Battles (June 30 and July 1) commanded by its lieutenant colonel.
He was placed in command of the 2nd Division, IV Corps during the Seven Days Battles where he again distinguished himself.
The following spring, he took his regiment to the Virginia Peninsula and fought in the Peninsula Campaign and the Seven Days Battles.
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The regiment and brigade served as the 1st Brigade of the 1st Division of the VI Corps, and participated in numerous battles from the June 27, 1862, Battle of Gaines Mill, Virginia, to the final Union assaults on Confederate positions at Petersburg, Virginia, in April 1865.
He took command of John J. Peck's 3rd Brigade, (55th New York, 62nd New York, and the 93rd, 98th, and 102nd Pennsylvania regiments) Couch's 1st Division, Keyes's IV Corps during the Seven Days Battles, after Peck was promoted to command of Silas Casey's Division of the same corps.
He received a commission as a brigadier general on July 19, 1861, and served first as a brigade commander in the (Confederate) Army of the Potomac, and then in David R. Jones' division of the Army of Northern Virginia through the Peninsula Campaign, Seven Days Battles, Northern Virginia Campaign, and Maryland Campaign.
Robert E. Lee was not satisfied with Whiting's performance during the Seven Days Battles and replaced him with Brig. Gen. John Hood.