Two Civil War era buildings from the Pensacola Navy Yard, a storehouse and the combination chapel/armory building, remain on what is now part of Pensacola Naval Air Station.

The Navy Yard's brick boundary wall, gatehouses, bulkhead, and wet basin from the Civil War period also survive.

The bulkhead and wet basin originally formed part of the Yard's ship construction and repair facility. Construction on the Navy Yard began in 1826. In the years leading up to the Civil War, it became a major facility for U.S. Navy shipbuilding, repair, and supply.

In January 1861, Southern troops from Florida and Alabama occupied the Navy Yard.

In September 1861, Union forces from Fort Pickens launched two raids directed against the Confederate held Navy Yard.

On September 2,the first Union raid destroyed a huge scuttled drydock which the Confederates had planned to refloat and sink in the channel.

The raid was accomplished without casualties on either side. The second Union raid, on September 14, resulted in the burning of the armed Confederate schooner Judah and the spiking of a Confederate Columbiad gun at the nearby battery. During this raid, Union forces suffered three dead and thirteen wounded,while Confederate forces suffered three dead and an undetermined number of wounded.

In November 1861 and January 1862, the Navy Yard suffered extensive damage when Union forces from Fort Pickens and U.S. Navy vessels engaged the Confederates in massive artillery duels.

In May 1862, Confederate forces withdrew from Pensacola, in the process stripping the Navy Yard of its valuable machinery and setting fire to the facility. Union forces reoccupied the Navy Yard cleared away the rubble and erected new structures.

Union Rear Admiral David G. Farragut inspected the Yard and concluded it could be repaired to serve as a naval depot for his West Gulf Blockading Squadron. The Squadron used the Pensacola Navy Yard as an operational base for the remainder of the Civil War.

Information provided by the Florida Department of State.