Located at the confluence of the St. Marks and Wakulla Rivers, Native Americans used the site of Fort San Marcos de Apalache for thousands of years. The park museum displays pottery and tools unearthed near the original fort.

The European history of this National Historic Landmark began in 1528 when Panfilo de Narvaez arrived in the area with 300 men. Beginning in 1678, the Spanish built two wooden forts at the confluence of the St. Marks and Wakulla Rivers. In 1739, they began the construction of the permanent stone fort of San Marcos de Apalache. The logs used were coated with lime to give the appearance of stone. The fort had stood only three years when it was burned and looted by pirates.

Not until 1718 did Captain Jose Primo de Ribera arrive to construct a second wooden fort. Construction began on the first stone fort in 1739. Progress was slow, and the fort was less than half finished when the Florida colony came under British rule in 1763.

By 1787, Spain regained control of the colony and the fort. Spanish rule was challenged in 1800 by a former British officer named William Augustus Bowles. General Andrew Jackson invaded the territory in 1818 and took San Marcos, but eventually withdrew, leaving the fort once again in Spanish hands, where it remained until 1821, when Florida became a U.S. Territory.

After General Andrew Jackson captured the Spanish strong point in 1818 and Spain subsequently ceded Florida to the United States in 1821, American troops intermittently occupied the fort, which they called Fort St. Marks.

In 1857-1858, a federal marine hospital was constructed for the care of yellow fever victims. By the time of the Civil War, the fort had been abandoned. Confederate forces occupied the site in 1861, strengthened it with earthworks and artillery batteries, and renamed it Fort Ward.

The fort provided protection for both the small blockade running port of St. Marks and the town of Newport, which contained a foundry and several mills. A small Confederate steamer equipped with two cannons, the CSS Spray, assisted in the area's defense.

Throughout the Civil War, the region was an active area for blockade running and salt production, and the Union navy had blockaded St. Marks since 1861. In July 1863, a Union navy expedition in small boats had attempted to move up the St. Marks River to capture Fort Ward and the CSS Spray, but withdrew when spotted by Confederate pickets.

In March 1865, a much larger Union expedition with a major objective of capturing St. Marks and Fort Ward met with defeat at the Battle of Natural Bridge.

Fort Ward remained in Confederate control until the end of the war when in May 1865 both the fort and the CSS Spray surrendered to a Union officer.

The property was acquired by the State of Florida in 1964 for use as a park facility. A visitor center and museum, constructed on the foundation of the 1850s marine hospital, provides interpretation with exhibits and artifacts. An interpretive trail includes the Confederate earthworks and the highest point on the site, the Confederate powder magazine.

Information provided by Florida Department of State Division of Historical Resources.