From the Civil War Florida site by Dale Cox.
A wartime sketch of the St, Marks lighthouse and Fort Williams appeared in the Frank Leslie's Illustrated Newspaper on February 11, 1862. It showed the USS Mohawk and the CSS gunboat Spray behind the fort.
The fort was named for Colonel J.J. Williams, a well-known planter from Leon County and was built to protect the mouth of the St. Marks River. It was an earthen fortification backed by timber and several pieces of heavy artillery were placed in it. It was sited on Lighthouse Point, just west of the lighthouse.
It was determined that the fort was isolated and could not easily be supported in an attack and the Confederates evacuated it in 1862. The defense of the St, Marks River was moved to the Spanish Fort San Marcos de Apalache which was in ruins, but a Marine Hospital was already on the site and could be used as barracks.