During the forty years of its existence, Fort Union hosted three different forts. The first fort was established in 1851 and became the Military Department Headquarters, replacing Fort Marcy in Santa Fe. The fort was known as the "guardian of the Santa Fe Trail," protecting travelers from Indian raids. The first fort was built near the foot of the long ridge (west of the current Visitors’ Center) and some ruins can still be seen. This fort is open once a year for visitors. In 1861, the Star Fort east of the first fort was built.
This second earthwork structure had an eight-pointed star design. This was built as a defense fort during the Civil War although no Confederate attacks ever took place at this site. In 1863, adjoining the Star Fort on the north, the third fort was built and became the largest military depot in the American Southwest. It functioned as a troop station for soldiers, and supply depot of goods and weapons for distribution to other western forts. The railroad reached Watrous in 1879, eliminating the need for defending trail trade. Fort Union closed in 1891.