After 1866, the fort's buildings were salvaged for other purposes and the area ultimately became the site of the Sacred Heart of Jesus Roman Catholic Church, surrounded by the developing residential neighborhoods of southeast Baltimore.

[1] After hostilities broke out between the United States and the Confederacy in 1861, Lt. Col. Henry Brewerton of the Union Army was charged in August of that year with strengthening the defenses of Baltimore.

[15][16] In addition, as the riots of April 1861 had proven, Baltimore itself was hardly a bastion of Union sympathizers, and so the fortifications served the dual role of enforcing the compliance of hostile Baltimoreans within, while protecting the city from Confederate attack from without.

One such incident uncovered a stock of gunpowder, bowie knives and short rifled muskets, worth at least $4000 (equivalent to $122,080 in 2023) in a stash below Canton.

[22] Service at Fort Marshall (as well as the other fortifications and encampments around Baltimore) served as useful and conveniently-supplied training camps for recently raised Union regiments, prior to their deployment to active theaters.

"[24] The fort's reputation for placidity was such that the 5th New York Heavy Artillery Regiment was able to offer "many inducements" in a recruitment advertisement in the Brooklyn Daily Eagle in 1862: "no long toilsome marches, no exposure in damp cold tents.

[27] One dramatic instance was that of Commander Woodhall of the Navy, whose body was flung 30 feet when he walked in front of a firing artillery piece, part of a salute for the tour of visiting army brass including Major General Benjamin Butler.

William Price Craighill was named the replacement for Lt. Col. Brewerton, and set about making upkeep repairs at Fort Marshall, which remained a military installation.

[34] Much of the building's lumber was salvaged by the Freedmen's Bureau, which used the material from Marshall and nearby Hicks U.S. Army General Hospital to construct more than sixty new schoolhouses.

"[37] A congregation of Baltimore German Redemptorists purchased the site of the former Fort Marshall in 1872-1873, and leveled the hill (which had given 'Highland Town' its name), building in its place the Sacred Heart of Jesus Roman Catholic Church.