Fort McRee was a bent elliptical fort built on a barrier island. At its widest points the fort was 450 feet by 150 feet wide. The wall that faced the channel was 366 feet long and about 35 feet above the water line during low tide. McRee held 128 cannons, including twenty-four 32 pounders. The fort was built before 1839 by William Henry Chase who oversaw the construction of all the Pensacola area forts.In early January 1861 Union troops located at Fort McRee destroyed about 20,000 pound of gunpowder and evacuated to Fort Pickens. On January 12th 1861 Confederate troops from Alabama and Florida occupied McRee.
On the morning of November 22nd 1861 Union batteries located at Fort Pickens opened on some Confederate steamers docked at the Navy Yard. The ships escaped with very little damage, while the Confederate guns located at Forts Barrancas and McRee returned fire on Fort Pickens. The USS Richmond and USS Niagara moved in firing on Fort McRee, shooting the Fort’s flagstaffs off. The Confederate fire was able to do some damage to the USS Richmond. Confederate General Braxton Bragg said of that day's battle, that "the houses in Pensacola, ten miles off, trembled from the effect; and immense quantities of dead fish floated on the surface of the lagoon, stunned by the concussion." At about 5 pm with the tide going out the two Union ships had to withdraw and the guns of McRee fell silent.The Battle took up again on November 23rd 1861 where it had left off. The Union side firing around 5,000 rounds of ammo into Fort McRee did extensive damage. Fort McRee’s Confederate commander Colonel John B Villepique sent word to Bragg that the fort was exposed, half his guns had been dismounted and the powder was in danger. The Confederate only returned about 1,000 shots, killing 2 and wounding 13 Union men. Fort McRee would survive the bombardment, but large chunks of wall were blown away or collapsed, and one powder magazine caved in. Six Confederate soldiers died in the action.