The Presidio de Nuestra Señora de las Caldas de Guajoquilla was established in 1752 on orders of Viceroy Revilla Gigedo at the site of present-day Jiménez, Chihuahua. The Marqués de Rubí, after his inspection of the late 1760s, recommended removal of the presidio to the Valley of San Eleceario as part of the new line of defense to be established by Hugo Oconór in the next decade. In 1789 the Presidio of San Elizario, named for St. Elzear-spelled Elzeario and otherwise in Spanish and Mexican documents-was moved up the Rio Grande to the hacienda of Tiburcios, the approximate site of the present town of San Elizario. The presidio was to protect the river settlements of Ysleta and Socorro and establish a colony of pacified Apaches. The perimeter enclosure with its thick adobe walls included quarters for four officers, barracks for forty-three soldiers, guardhouses, corrals, storerooms, and a chapel.
In the first decade of the nineteenth century Spanish frontier officials became increasingly concerned about the American intrusion on Spanish New Mexico. In 1807 Zebulon Montgomery Pike, a United States Army captain, was arrested by Spanish officials on the headwaters of the Rio Grande above Santa Fe and charged with entering Spanish territory illegally. He was brought under heavy guard to the presidio of San Elizario, where he remained for three days before he was taken to Chihuahua. After his release Pike published his comments on the commercial possibilities of Spanish New Mexico, and his publication became popular in the United States. By 1810 Spanish officials had become thoroughly aroused by the increasing number of American traders arriving in Santa Fe, many of whom suffered arrest, confiscation of merchandise, and confinement in San Elizario Presidio. After the Mexican War of Independence ended in 1821, the Apache colony numbered more than 1,000, but it quickly disintegrated after 1831, when Mexican officials terminated the ration program. Meanwhile, San Elizario Presidio had provided the nucleus for the development of a town that grew to more than 1,000 by 1841. The Rio Grande had formed a new channel south of Ysleta, Socorro, and San Elizario, thus placing these settlements on what amounted to an island, known as La Isla or "the Island." Living conditions were primitive, and poverty was widespread.
During the Mexican War an American army of Missouri volunteers under the command of Col. Alexander Doniphan routed a Mexican force at the battle of Brazito some twenty-eight miles northwest of El Paso del Norte on December 25, 1846, and entered the Mexican town. Two American officers who visited San Elizario and whose diagram of the presidio is included in the classic Butterfield Overland Mail, 1857–1864 (1947), found the presidio deserted and in ruins, though most of the walls were still standing. They also discovered a number of bloody bandages, evidence that Mexicans wounded in battle received medical attention there. In accordance with the Treaty of Guadalupe Hidalgo of February 2, 1848, the Rio Grande became the boundary between the United States and Mexico, and the Island became a part of the United States. Two companies of United States infantry were stationed at the old presidio from 1849 to 1851, and when El Paso County was established in March 1850 San Elizario was the county seat. In 1851 John Russell Bartlett, the boundary commissioner, found the old presidio in ruins. The settlers had dismantled the walls and buildings to obtain adobe to construct their own residences.