During most of the Civil War, the area surrounding Marlborough was occupied by Union forces.
Windmill Point, a union field hospital, was located on Marlborough Point, at the site of John Mercer’s long ago windmill. In his army letters, U.S. Christian Commission field agent John A. Cole described his visit to the hospital: “I have just come from Windmill Point Hospital where are about 4,000 sick soldiers, some of them have suffered terribly and many die daily…. many lives I believe have been saved within the past three weeks and many souls have passed from darkness into light.” (Feb. 10, 1863)
Some of those who died at Windmill Point Hospital were buried on "Marlboro Point." They were later reburied in the Fredericksburg National Cemetery.
The Potomac River was the site of one of the first naval engagements in the Civil War. Not very far from Marlborough at Aquia Landing, Confederates built their defenses to cover the Richmond, Fredericksburg, and Potomac Railroad terminus and steamboat landing. A battery of five Confederate guns was stationed at Marlborough Point. On August 23, 1861, Colonel R. M. Cary, Thirtieth Virginia Infantry, gave an action report from his position at Marlborough Point, in which he detailed a 40-minute encounter in which his officers and men "behaved with proper coolness and deliberation." Aquia Landing was abandoned by the C.S.A. in March of 1862 to Union forces who put their own batteries in place.