One of the two Confederate batteries at Fort Ward was built here, into the stonework of the old Spanish bombproof. The Union Navy attempted to attack the fort on a couple of different occasions, but was never able to make it up the narrow channel from the Gulf of Mexico. The Confederate Navy, incidentally, regularly used the same channel and often based a small gunboat, the C.S.S. Spray, at the fort. The most serious attempt on Fort Ward was made in March of 1865, when a Union expedition intending to take the works from the rear was turned back in the nearby Battle of Natural Bridge

During the 1860s, stone from the old Spanish fort of San Marcos de Apalache was used to construct a marine hospital on the site. When the Confederates reoccupied San Marcos and built Fort Ward, they used the hospital as a barracks. This view shows the foundations of the old marine hospital, on top of which the state has constructed a museum