Troy Spring was purchased by the state of Florida in 1995. Prior to that time, Troy Spring was only accessible by boat or by navigating dirt roads and cow pasture gates. Many people still remember when they could drive their boats all the way into Troy Spring to enjoy fishing, swimming, diving and the company of others. Today, boaters can still enter the park from the river boat dock; however, a paved entrance road has become the more popular access route.
The spring is the historic site of what remains of the steamship, Madison. In the mid-1850s Captain James Tucker had his ship, Madison, built with a very shallow draft especially intended for the frequently changing water levels of the Suwannee River. For many years, the ship served as a floating mail service and trading post. In 1861, at the beginning of the Civil War, it was used by the Confederate forces as a privateer and jerry-rigged gunboat. In 1863, it was scuttled in the spring, upon the order of its owner, to prevent it from getting into the wrong hands. Today, some of the metal spikes and the remnant keel rib timbers that were part of its hull can be seen below the spring surface.