One of the three major forts designed to protect the mouth of the Columbia River,  Fort Stevens was constructed on the Oregon side of the river's mouth. The three forts—Fort Stevens, and, in Washington, Forts Columbia and Canby—were authorized by an act of Congress in February 1862 to provide "for the defense in Oregon and Washington Territory at or near the mouth of the Columbia River." While the original purpose was to protect the river from Confederate commerce raiders (such as the C.S.S. Alabama), the Civil War was over before Fort Stevens was fully operational. Fort Stevens was named for a former governor and congressional delegate of Washington Territory, Isaac I. Stevens , who was killed in 1862 at the battle of Chantilly. Stevens had been a popular figure in the Pacific Northwest, and the naming of the fort was seen as a fitting tribute.

After the Civil War, Congress reduced the army's budget. At Fort Stevens that meant funding maintenance, some construction, and a small resident military force. In 1884-1898, the Army Corps of Engineers took over Fort Stevens to use as a base for its work to improve the Columbia River Channel. It was not until 1896 that the U.S. Army began to expand and modernize Fort Stevens as a coastal defense installation. The last of the concrete gun emplacements, Battery Russell, was completed in 1904.

Fort Stevens saw no combat during World War I, and its cannons were fired only in practice or when rendering honors to visiting warships, such as French cruiser Jeanne d’Arc and German cruisers Karlsruhe and Emden in the 1930s.

The fort was the home of the 18th Coast Artillery Regiment, augmented by the Oregon National Guard’s 249th Coast Artillery Regiment, which trained at the fort during each summer's muster and on weekend duty throughout the year. When President Franklin Roosevelt federalized the National Guard in September 1940, the 249th reported to the three Columbia River forts, where they provided support for the 18th Coast Artillery Regiment as it was transferred, a battery (company) at a time, to more active duty. Despite several submarine attacks at the mouth of the Columbia River in December 1941, Fort Stevens’ guns remained silent. Twice the Japanese submarine I-25 attacked oil tankers at or near the mouth of the Columbia, damaging the tanker S.S. Connecticut by torpedoing the empty oiler.

The most significant event in the fort’s history took place on the night of June 21, 1942, when the I-25, under the command of Commander Tagami, opened fire on Fort Stevens with its 5.5 deck gun. Seventeen shells landed on the military reservation without causing significant damage, and once more the fort’s guns remained silent—among other reasons, the submarine was believed to be out of range. Fort Stevens was the only military installation in the contiguous United States to be shelled by a foreign enemy warship since the War of 1812. A stone monument south of Battery Russell commemorates the event.

After its decommissioning in 1947, Fort Stevens is now one of the most popular units of the Oregon State Parks and Recreation Department and is listed on the National Register of Historic Places. Preserved on the grounds are parts of the fort, a museum, and reconstructed earth ramparts of the Civil War fort. The campgrounds and beautiful beaches belie the fort’s place in history. It has been the scene of shipwrecks and enemy ships shelling bucolic shores, but its main historical significance was as an active military installation defending the Great River of the West.