The defense of the St, Marks River now lay with the old San Marcos de Apaliche, six miles upriver from the Gulf of Mexico.
The design of the old Spanish fort was altered and the remaining old walls were used to back up heavy earthworks. Fort Williams was then somewhat dismantled and what remained of it was later burned by the Union Navy. iin the attack by the USS Tahoma and Somerset June 15, 1862. However, the reports of these two ships made it sound like there was an engaement, which, if this is to be believed, would not have happened if the fort had been abandoned already.
There is no trace remaining of Fort Williams today. The lighthouse survived the war and still stands