After the War of 1812, the federal government began building what was known as third system brick coastal defense forts. Construction began on Fort Morgan in 1819, but due to its isolated location, it was not completed until 1834. Skilled masons, many of whom were enslaved African Americans, built the fortification which contains more than 46 million cubic yards of bricks.

Fort Morgan was active during four wars: Civil War, Spanish-American War, World War I, and World War II.

The fort is historically significant for its Civil War role in the Battle of Mobile Bay. It is here on August 5, 1864, Union Admiral David Farragut ordered his fleet to charge the heavily mined bay. (At the time, tethered naval mines were known as torpedoes.) "Damn the torpedoes!" said Farragut, "Four bells. Captain Drayton, go ahead! Jouett, full speed!" After the Battle of Mobile Bay, soldiers at Fort Morgan endured a two-week siege by Union forces before surrendering on August 23, 1864.

Designed to control the main ship channel into Mobile Bay, the star shape of Fort Morgan allowed its defenders to bring a heavy concentration of artillery fire on an enemy fleet as it approached the fort and moved into the bay. The fort was also designed with extensive land defenses to enable it to withstand a siege.

The introduction of rifled artillery and steam-powered warships during the Civil War made masonry fortifications like Morgan obsolete. This was dramatically demonstrated on August 5, 1864, when Union Admiral David Farragut led his fleet past the guns of defenders and into the bay with the loss of only one ship. Following the Civil War, the Army moved slowly to improve the nation's coastal defenses. It was not until the 1890s that major improvements were undertaken. The Board of Fortifications, or Endicott Board, recommended five modern gun batteries as well as naval mines at Fort Morgan. Constructed between 1895 and 1904, these batteries housed 19 guns and mortars -- the most modern weapons of the day. The concrete batteries were manned during the Spanish-American War and World War I. The military occupied Fort Morgan more than two years during World War II. By that time the concrete batteries, like the brick fort before them, were no longer the primary defensive positions. The military returned the fort to the state after the war, ending an era of coastal defense.

A one room structure from the Civil War remains. It is connected to the lighthouse keeper’s house that was built as an addition in 1872. The five remaining wooden buildings date to the beginning of the 20th century. Between 1898 and 1910, the military greatly expanded the base. The surviving buildings were part of a large support complex that numbered almost 100 structures. The buildings were originally designed for use as coast artillery officer's quarters kitchen, staff officer's quarters, hospital steward's quarters, post bakery, and post administration building.