It is situated on the Rio Grande (Río Bravo del Norte) River, on the opposite side of the U.S.–Mexico border from Ojinaga, Chihuahua.

By 1200 CE, the local Native Americans had adopted agriculture and lived in small, closely knit, La Junta Indians settlements, which the Spaniards later called pueblos.

On December 10, 1582, Antonio de Espejo and his company arrived at the site and named the pueblo San Juan Evangelista.

Five Jumanos towns were located along the Rio Grande to the north of the junction, consisting largely of permanent houses.

[6] In 1683, Juan Sabeata, the chief of the Jumanos, reported having seen a fiery cross on the mountain at Presidio and requested that a mission be established at La Junta.

Ben Leaton and Milton Faver, former scalp hunters for the Mexican government, built private forts in the area.

[9] During the Mexican Revolution, General Pancho Villa often used Ojinaga as his headquarters for operations and visited Presidio on numerous occasions.

[citation needed] As a result of Pancho Villa's force's raid and capture of Ojinaga on January 10, 1914, many Mexican army troops and civilians fled to Presidio seeking safe-haven.

U.S. forces detained 2,000 Mexican refugees in Presidio, eventually marching them north 60 miles to Camp Marfa.

In 1930, the Kansas City, Mexico and Orient Railway reached Presidio and the Presidio–Ojinaga International Rail Bridge was built.

At the end of 1988, Presidio experienced a population boom, due in part to previously undocumented immigrants enrolled in the amnesty program.

[needs update] The increased bridge capacity is projected to meet higher traffic, mainly commercial and agricultural in nature.

The Rio Conchos flows in a northeasterly direction from its source in the Sierra Madre in the state of Chihuahua, Mexico.

Commonly referred to as "La Junta" (the joining), the two rivers resulted in plentiful water, creating a flood plain that is ideal for farming.

Plans are underway to open Chinati Mountains State Natural Area, 15 northwest of Presidio, along FM 170.

Big Bend Ranch State Park is adjacent to Presidio with Fort Leaton serving as a facility to purchase use permits.