The historic battlefield site was named for its true geologic feature that provides a crossing point at a section where the St. Marks River goes underground for a distance before reappearing, therefore forming a natural bridge. The property is also the site of Florida' second largest Civil War battle. It is listed on the National Register of Historic Places and cited as one of the Top 10 endangered Civil War sites in the United States by the Civil War Preservation Trust.
In 1865, during the final week of the Civil War, the battle at Natural Bridge preserved Tallahassee as the only Confederate capitol east of the Mississippi that did not surrender to Union forces.
In February 2009, the state of Florida purchased nearly 55 acres of land adjacent to the original property to protect a first magnitude spring.