Fort Clinch occupies approximately 1,121 acres of land on northern Amelia Island. With over 8,400 feet of shoreline, the fort guards the entrance to the freshwater St. Mary's River and Cumberland Sound. The fort also has approximately 4,000 feet of coastline with the Atlantic Ocean. Acquired by the state parks system in 1935, the Civilian Conservation Corps (CCC) was responsible for some of the initial development of the park.

The site on which Fort Clinch stands has been occupied by various military troops since 1736. Construction on the existing structure began in 1847 as part of the Third System Fortifications building program, which was also responsible for the construction of nearby Fort Pulaski in Georgia. Fort Clinch was named after General Duncan Lamont Clinch who was a prominent participant in Florida's Second Seminole War.

Fort Clinch was occupied by Confederate forces upon the beginning of the Civil War in 1861. The Union then took over the fort in 1862 after General Robert E. Lee ordered the withdrawal of the Confederates. Fort Clinch never saw any battle time during the Civil War and remains remarkably well preserved to this day.

The fort offers picnicking, camping, saltwater fishing, shelling, hiking, and nature study on its grounds. Fort Clinch also features a nature trail with towering sand dunes and wide array of native plant and wildlife.