Nuestra Señora del Refugio Mission, the last of the Spanish missions in Texas, was founded on February 4, 1793, by Franciscans of the College of Nuestra Señora de Guadalupe de Zacatecas, as part of prefect Manuel J. de Silva's ambitious plan to pacify and convert all the Indians living along the Texas coast. In 1791 Fray Silva and Fray José Francisco Mariano Garza toured the Matagorda Bay region to discover a suitable site for the conversion of the Karankawa Indians. Missionaries had attempted to settle and convert to Christianity groups of Karankawas at Nuestra Señora del Rosario and Nuestra Señora del Espíritu Santo missions, but the Indians deserted and refused to return. However, the deserters promised the visiting priests that they would come to a mission if one was established on the Texas coast. The Indians helped choose the mission site, in an area known as El Paraje del Refugio "Place of Refuge," at a site on Goff Bayou now in Calhoun County, north of Mission Lake and a half mile northwest of the site of present Long Mott. The new Texas mission was named Nuestra Señora del Refugio and was to serve the region surrounding Matagorda Bay.
The mission was intended to teach European values and Christianity to the Indians as well as the industries of agriculture and cattle raising. However, from the time of its founding, the priests and the neophytes were faced with a variety of problems. An inadequate food supply and lack of tobacco caused unrest among the Indians. Also, construction of the mission buildings was slow, and the buildings were not watertight. At the end of its first year, the mission consisted of only six small wooden buildings with tule roofs, a corral for the cattle, a large frame shed, and a surrounding stockade. Indian attacks, led by Karankawa chief Fresada Pinta, contributed to the urgency of the need to move to a more environmentally suitable and better protected site. In June 1794 the mission moved to Rancho de los Mosquitos, on Mosquitos Creek, about halfway between the juncture of the San Antonio and Guadalupe rivers and the mouth of the Guadalupe. Despite the move, conflict with Fresada Pinta continued, the food supply remained inadequate, and many of the mission Indians left to search for food along the coast. In January 1795 the mission moved to its final location at the site of the present town of Refugio, a location considered better suited for farming. Retaining its original name, Nuestra Señora del Refugio Mission was formally dedicated by Silva on January 10, 1795. Temporary relief from food shortages arrived in the spring of 1795, when 227 cattle were delivered, soon followed by 139 more. A census taken in October of that year reported a population of 82 Indians, down from the 138 Indians present at the founding of the original mission. By the fall of 1796 there were 175 Coco and Karankawa Indians at the mission, but more than half of that number had deserted the Rosario Mission. Conflicts arose among the Indians at Refugio, and again many left for the coast. The mission became a focus of attack by the Comanches, who invaded and stole livestock. Despite these difficulties, the construction of the mission was nearly completed by 1799. Most of the buildings, including workshops, a granary, and living quarters for the padres, the Indians, and the mission's few soldiers, are believed to have been constructed of driven poles with adobe walls and thatched roofs. Only the church and the blacksmith shop are believed to have been of stone. The church had a wooden roof and a tile floor. A stockade surrounded the mission and helped protect the soldiers and inhabitants during times of Indian attack.
Despite annual attacks by Comanches and other nonmission Indians, the mission reached a population of 224 in 1804. In 1807 Rosario Mission was ordered closed, and its Indians were officially merged with those at Refugio. However, continued attacks by Comanches and Karankawas and frequent internal conflicts among Refugio Indians, combined with an unstable food supply, led to the gradual abandonment of the Refugio Mission. On July 10, 1824, Governor José Antonio Saucedo issued orders to secularize and close Refugio Mission, and the mission's surviving possessions were carted away to La Bahía (Goliad). Between 1825 and 1829 attempts were made to restore the mission, but they failed. On January 7, 1830, when fewer than two dozen Karankawa and Coco Indians remained attached to the mission, the Mexican government decreed that the earlier secularization order be executed, and the mission was finally abandoned and left to ruin.
Baptismal records for the mission's early years no longer survive. Records for the years 1807 through 1828 indicate a total of 214 baptisms performed by the mission's priests. Of those receiving the sacrament, sixty-nine were Spanish children, and the rest were Indians. Fray Miguel Muro added a notation in the baptismal records, stating that the baptisms administered after July 1824 were performed in the parish of La Bahía "because the minister could not subsist in the mission [of Refugio] on account of the hostilities of the Comanches." Although the Karankawas were the most largely represented group of Indians at Refugio Mission, baptismal records reveal the presence of others, including Copanes, Cocos, Cojanes, Guapites, Malaguitas, Piguiques, and Pamiques. Burial records of 1807 to 1825 indicate approximately forty-three Spanish families also resided in the vicinity of the mission during the period.
When Irish settlers moved into the mission area during the 1830s, they named their town for the mission, and the mission ruins were probably used as building materials for their new settlement. Much of the mission site is presently owned by Our Lady of Refuge Catholic Church. Traces of the foundation of the mission can be found beneath the present church and the surrounding lawn. There are no visible remains at the earlier mission sites.