Between March 1 and 3, 1865, a Union flotilla arrived in Apalachee Bay. General John Newton and Naval Commander William Gibson had a joint assault plan in mind to cripple Confederate forces. On March 3, 300 seamen surprised Confederate pickets and captured the East River Bridge, four miles north of the St. Marks lighthouse. The following day, Navy gunboats commanded by Gibson ran aground in the shallow waters of the St. Marks River. Gibson spent the next two days desperately trying to get upstream to Port Leon but was unsuccessful.

Gibson’s unexpected delay provided just enough time for a Confederate messenger to travel to Tallahassee and warn the citizens of the danger to the Capitol caused by the Union landing. In an effort to defend the Capitol, every man and boy who could bear arms volunteered to join the thin ranks of the Confederate Army. The forces were made up of wounded confederate soldiers home to recuperate, men as old as 70 and cadets as young as 14 from West Florida Seminary (now Florida State University). The Confederate troops, commanded by General William Miller, were taken to Newport to prepare a defense.

On March 5, Union General Newton advanced past the East River Bridge, causing Confederate troops from the Fifth Cavalry to withdraw to the Newport Bridge on the St. Marks River. The Confederate cavalry was joined by the volunteers from Tallahassee, where they gained enough strength to force Newton to take a round-about route to Natural Bridge. Miller, who had second-guessed Newton’s attempted surprise crossing, sent Confederate forces under Lt. Colonel George Scott on an overnight march to defend the crossing.

In the pre-dawn hours of the following day, a series of skirmishes lasting about 10 hours occurred along the narrow natural bridge. Confederate forces, made up of 500 to 700 men, fought off three major attacks and several minor attempts by Union forces of nearly equivalent strength. The Union troops, having decided that the bridge was impassable, began a hasty retreat.

By sundown on March 7, Union soldiers were in the protection of their own fleet. Newton, feeling that he had not been adequately supported by the Navy, took his troops back to Key West. Union losses totaled 21 killed, 89 wounded and 38 captured. Confederate losses were three killed and 22 wounded.