In spring 1863, the Confederates moved this base north Shreveport, just before a U.S. Army-Navy operation captured Alexandria on May 7. Union forces abandoned the city by summer
In spring 1864, Alexandria became the target of Union Gen. Nathaniel Banks' Red River Campaign. In March, a combined land and sea operation captured Fort DeRussy, downriver from the city, and the Union reoccupied the city.
Banks marched west where he was defeated by Confederate troops under Gen. Richard Taylor. He then retreated to Alexandria on April 9, where low river levels trapped the naval fleet. Troops constructed a dam to raise the water level and the gunboats escaped. The Union Army withdrew from Alexandria May 13, burning part of the city as they departed. on
By 1880, a brick wall surrounded the cemetery. A brick Second Empire-style lodge housed the superintendent and his family. Large artillery pieces flanked the cemetery entrance. Trees planted along the road created a shady avenue from the main gate to the flagstaff at the center of the cemetery. In 1931, the old lodge was razed and the current one was constructed.
In 1909, a contractor, using local labor, exhumed more than 3,000 dead from this cemetery. Five freight-train cars transported the remains to Alexandria. The identified remains were interred along the northwest wall, and the area designated Section B. Unknown remains were placed in a mass grave on the southeast side of the flagpole circle. The federal government erected a group monument on this grave.