The lighthouse was the site of several military operations during the Civil War. In June 1862, the Union navy shelled the area, destroying the small Confederate fortification of Ft. Williams located near the lighthouse. A year later the navy returned and burned the lighthouse's interior steps, trying to prevent its use as a Confederate lookout tower. The tower stairs were rebuilt, then burned again. This cycle continued throughout the war. In March 1861, the Union fleet became stuck on a sandbar near the lighthouse delaying the landing of Union General Newton's forces. This allowed the Confederates time to gather sufficient troops to stop the Union forces and prevent them from capturing Talhassee.