In 1722 the Marqués de Aguayo authorized Father Agustín Patrón y Guzmán to establish Nuestra Señora del Espíritu Santo de Zúñiga Mission, commonly called La Bahía, probably on Garcitas Creek at a site in what is now Victoria County. The mission, one of the oldest and most successful in Texas, was to serve area Karankawa Indians: the Cocos, Copanes, and Cujanes. The Spanish governor fixed April 10, 1722, as the official day of establishment. The mission was placed in the care of the Franciscans from the College of Nuestra Señora de Guadalupe de Zacatecas and established in connection with Nuestra Señora de Loreto Presidio, which the Aguayo expedition had established a year earlier on the ruins of La Salle's Texas Settlement. The name of the mission, which appears in Spanish records also as La Bahía del Espíritu Santo de Zúñiga, was a reference to its location on La Bahía del Espíritu Santo (the Bay of the Holy Spirit, now called Matagorda Bay and Lavaca Bay) and also honored Báltasar de Zúñiga, viceroy of New Spain. The establishment remained at its original site only about four years and was relocated at least twice. As early as April 1725 the padres recommended moving it and its presidio to a location more favorable to their missionary efforts. They had been unable to induce the wandering Karankawas to accept Christian teachings or stay at the mission, and there had also been incidents of ill feeling and violence between the Indians and the Spaniards. Nuestra Señora del Rosario Mission was later established on the San Antonio River to minister to the Karankawas.
By April 1726 La Bahía had been relocated about ten leagues west among the Aranama and Tamique Indians at a site on the Guadalupe River now called Mission Valley in present Victoria County. The new structure was built from the area's abundant timber and from stone quarried some ten leagues distant. At least two dams were constructed within a five-mile radius of the mission to direct water from the Guadalupe River and Mission Creek through stone acequias into fields for crop cultivation, though the padres soon found that the normal rainfall was adequate. The mission's associated ranchería (small village) or possibly its visita (country chapel) was constructed of mortared stone some twelve miles downriver on a bluff called Tonkawa Bank near a popular low-water crossing. A more controversial archeological interpretation of this site suggests that the mission itself was first moved to Tonkawa Bank before being moved upriver to the Mission Valley site, possibly because of flooding. The presidio was also moved from Garcitas Creek to a site on the Guadalupe River that later became Fernando De León's Rancho Escondido.
For the next twenty-six years the mission prospered on the banks of the Guadalupe River. The padres were much more successful here with their attempts to baptize and instruct the Indians, despite incidents of desertion; inevitably some Indians fled from the difficulties of adjusting to the regular routines of mission life. A strict moral code was enforced, and the missionaries implemented a complex political structure in which Indians were elected to custodial positions. With the aid of the Indian wards, the padres produced sufficient corn and hay for both the mission and presidio and had enough to export some to the East Texas and San Antonio de Béxar settlements. The main industry, however, was livestock raising and exporting, particularly of cattle and horses. The animals grazed and roamed on the prairies bordered by the Guadalupe and Lavaca rivers on the north and the San Antonio River on the south. In its horse and cattle business the mission laid the foundation for one of the characteristic Texas industries. Later, during the Mexican period , ranchers of prominence such as Martín De Léon built fortunes from the thousands of cattle and horses still roaming wild, descended from those at La Bahía.
The Spanish effort to keep possession of the territory north of the Rio Grande led the royal government to authorize José de Escandón's expedition to evaluate ways to halt English and French encroachment. After exploring the area in January and February of 1747, Escandón recommended moving the La Bahía presidio and mission to the San Antonio River to protect the main road from Mexico to Bexar and East Texas. The area was similarly suited to crop and stock raising, and timber, stone, lime, and other building materials were plentiful. The viceroy ordered the mission and presidio moved to this location, named Santo Dorotea by presidio captain Joaquín de Orobio y Basterra, when he camped there about February 5, 1747, during the Escandón expedition. The move from the Guadalupe to the San Antonio river occurred in the fall of 1749, probably in October, since a government report dated November 16, 1749, shows that the removal had been accomplished. Orobio was charged with this task and, despite being denied extra assistance, managed to traverse the creeks and wooded prairies with oxcarts and mules.
Espíritu Santo was temporarily reconstructed with wood and caliche, but by 1758 Father Francisco Xavier de Salazar reported to Governor Jacinto de Barrios y Jáuregui that the mission complex had been rebuilt of stone and mortar, though the mission's Indian population, which in May 1758 was forty-nine warriors, fifty women, and seventy-nine children, was still living in jacals. The missionaries used a manual of Indian words compiled by Father García of San Francisco de la Espada Mission to communicate with these people because of the difficulty of teaching them Spanish. The padres focused their missionary work upon the local Aranama, Tamique, Tawakoni, and Tonkawa Indians with some success, though some desertion continued. By the early 1760s Apaches began preying upon the mission's cattle and inhabitants, but the mission still prospered. During his inspection tour of 1767–68, Gaspar José de Solís recorded that Espíritu Santo Mission was smaller but in better condition than its nearby sister mission, Nuestra Señora del Refugio. The royal La Bahía presidio was within sight across the San Antonio River, which was crossed by canoe and had a large stock of fish. Solís complimented the sole priest's hard work and zeal in ministering to and educating the Indians and the presidio soldiers as well. He noted large herds of cattle, horses, mules, oxen, and sheep and cropland yielding corn, cotton, melons, potatoes, peaches, and figs. The mission population, including Aranama, Tamique, Piguique, and Manos de Perro Indians, was some 300, he recorded, and since the mission was founded 623 baptisms and 278 burials had occurred there.
Espíritu Santo is traditionally recognized as the first great cattle ranch in Texas. Historians estimate the total number of cattle and horses belonging to the mission and the settlers of La Bahía to have reached some 40,000, though those actually branded in 1778 numbered something over 15,000. When Mission Rosario was temporarily abandoned in 1779 and again in 1781, its herds of cattle were also combined with those of Espíritu Santo. These herds were driven by Indian cowhands to other missions and to East Texas and Louisiana and exchanged for corn and other supplies.
By the 1790s conditions at the mission had deteriorated, however. Clashes between the various tribes who visited the complex increased, as did raids by Lipan and Comanche Indians. The few soldiers at the presidio were unable to protect the mission settlement adequately. The government's lack of understanding of conditions in the Provincias Internas caused passage of unsatisfactory and injurious policies. Increasingly, Anglo pioneers infiltrated the area.
Espíritu Santo, like all Texas missions, was not intended to be a permanent institution. With the secularization decree of April 10, 1794, the Spanish government declared that the padres had accomplished their purpose, the mission property and land were to be distributed among the Indian converts, and the church turned over to secular clergy. Governor Manuel Muñoz petitioned the government for a five-year extension for Espíritu Santo, as well as for the nearby Refugio and Rosario missions, believing that the Indians there were incapable of managing their own affairs. Authorities in Mexico granted the request on May 10, 1797, though internal turmoil in the government allowed an even longer extension. Indeed, the various decrees of secularization issued from Spain from 1793 to 1813 seem hardly to have affected La Bahía. But the political unrest in Mexico finally exacted a toll. Secular priests were not available to assume the Franciscans' duties, royal presidio troops were not reinforced, and Lipan and Comanche depredations increased. La Bahía was affected by episodes of the Mexican War of Independence against Spain, notably Miguel Hidalgo y Costilla's revolt in 1810, the Gutiérrez-Magee expedition of 1812–13, and Henry Perry's 1817 campaign. Espíritu Santo managed to survive these trials but by 1821 was left impoverished and near ruin, its Indian wards having deserted and returning only occasionally.
After Mexico achieved independence from Spain in 1821, the new government pursued the secularization policy. Still, the Franciscans tended La Bahía, Refugio, and Rosario missions as late as February 19, 1826, though all provisions for maintenence had stopped and the Franciscan order had recalled its friars. Secularization instructions were again issued on March 28, 1827, though the final instructions came only in the spring of 1829. Even so, two Franciscans refused to leave and remained as parish priests, ministering to settlers at Goliad (as the newly designated villa of La Bahía was called in 1829) and at nearby Victoria and Refugio. In February 1830 Espíritu Santo, Refugio, and Rosario were secularized, the last missions in Texas to comply with the secularization orders.
The valuable lands of Espíritu Santo, intended eventually for the Indians, were increasingly desired by Mexican and American colonists settling in the area, notably those locating at Goliad, in De León's colony, and in the Power and Hewetson colony. La Bahía assumed a critical role during the Texas Revolution, though the events centered around the presidio rather than the mission, which had fallen into ruin. On January 12, 1841, the Congress of the Republic of Texas recognized the ownership of the Catholic Church of the old mission, though the church failed to get possession of it. In 1846 and 1847 the Goliad city council approved the disposition of the mission, which local residents popularly called Aranama Mission; the council reserved the structure and twenty acres of land for county or college buildings but also granted citizens the right to carry away loose rocks. Part of the mission ruins and grounds were used by Hillyer Female College, established as a Baptist institution in 1848, and by Aranama College, founded in 1856 under the auspices of the Western Presbytery of the Presbyterian Church and given the mission's popular name.
On March 24, 1931, the city of Goliad and Goliad County transferred the site to the state, which agreed to preserve it as a historical park. During Franklin D. Roosevelt's New Deal (1933–41), federal public-works projects conducted archeological, historical, and architectural research at the mission site, and its buildings were then restored with local Civilian Conservation Corps labor under the supervision of the National Park Service and the University of Texas. Additional reconstruction occurred in the 1960s, and by 1987 the mission appeared as it did in 1749. A Texas Centennial marker was erected there in 1936, a Texas Historic Landmark Medallion was affixed in 1969, and in 1977 the mission was listed in the National Register of Historic Places. The beautifully restored Espíritu Santo mission is the focus of Goliad State Historical Park and is administered by the Texas Parks and Wildlife Department.
The former locations of Espíritu Santo mission have also been investigated. The original site (known as the Keeran Archeological Site) on Garcitas Creek near present Inez in Victoria County, though lost until the early twentieth century, was later excavated by the Texas Memorial Museum in 1950 and by Kathleen Gilmore in 1973. Though on private property, it received a Centennial marker in 1936 and was listed in the National Register of Historic Places in 1971. The second location, near present Mission Valley in Victoria County and also on private property, had not yet been archeologically investigated in 1988, though remnants of a stone dam on Mission Creek and a partly stone-lined acequia were visible. The site of the mission's associated visita or ranchería (called Tonkawa Bank Archeological Site) is located near the Guadalupe River in Victoria's Riverside Park and was excavated in the 1970s by John L. Jarratt and Jim Sutton. The Mission Valley site was listed in the National Register of Historic Places in 1980, the Tonkawa Bank site in 1981. Both have historical markers.