Fort Pickens was of a Pentagonal design, with broader western walls to provide a wide range of fire over the bay.

The fort had a counterscarp to the east side exclusively, to create a defensive moat in the event that a land invasion came from the west.

The westernmost Bastions were also equipped with mine chambers, to be detonated in a last-ditch-effort to save the fort from invaders.

On the night of 20 January 1858, the USCS Robert J. Walker was at Pensacola when a major fire broke out at Fort Pickens.

The cutter's men and boats, joined by the hydrographic party of the United States Coast Survey steamer USCS Varina, rallied to fight the fire.

On January 10, 1861, the day Florida declared its secession from the Union, Slemmer destroyed over 20,000 pounds of gunpowder at Fort McRee.

Slemmer defended the fort against threat of attack until he was reinforced and relieved on April 11, 1861, by Colonel Harvey Brown and the USS Brooklyn.

The fort was further reinforced by Colonel William Wilson and elements of the 6th New York Infantry Regiment by late June 1861.

[3] The Confederates attacked the Fort on October 9, 1861, in the Battle of Santa Rosa Island, with a force of a thousand men.

Running low on supplies, and with dwindling morale, the Confederates began to doubt their chances of success in the Battle of Pensacola.

From October 1886 to May 1887, Geronimo, a noted Apache war chief, was imprisoned in Fort Pickens, along with several of his warriors.

Instead of many guns concentrated in a traditional thick-walled masonry structure, the Endicott batteries are spread out over a wide area, concealed behind concrete parapets flush with the surrounding terrain.

The use of the accurate, long-range weapons eliminated the need for the concentration of guns that was common in the Third System fortifications.

[5] The damage was relatively confined to Bastion D, but the foundations were torn away along with sections of the walls to allow for easier access to the batteries.

Many of these batteries were built across the nation, all with the same design, to replace the role of light artillery formerly held by the 3-Inch M1903 guns.

The 12-inch barbette guns that were in place were kept, but 17 feet of concrete was added to create a bomb proof bunker.

Although improved in the late 19th century during the run-up to the Spanish–American War, the fort was struck by a hurricane on September 26–27, 1906 that destroyed most of the newer structures erected since 1898.

In May 1862, after hearing that the Union Army had taken New Orleans, Confederate troops abandoned Pensacola and Fort Barrancas.