The San Marcos River rises at Aquarena Springs in San Marcos, Hays County (at 29°56' N, 97°55' W). The Blanco River joins the San Marcos four miles downriver from the springs. The San Marcos flows southeast for seventy-five miles, forming the boundary between Guadalupe and Caldwell counties and part of the boundary between Gonzales and Caldwell counties, before reaching its mouth on the Guadalupe River, two miles west of Gonzales (at 29°29' N, 97°28' W). The history of the river's name is complicated. In 1689 members of Alonso De León's expedition gave the name San Marcos to the first considerable river east of the Guadalupe, which scholars now believe to have been either the Colorado River or the Navidad River. Later Spanish explorers applied the name San Marcos to the first considerable river beyond the Guadalupe to the north and west-that is, to the present San Marcos River. Domingo Terán de los Ríos, however, is thought in 1691 to have called the San Marcos the San Agustín, and the Marqués de Aguayo in 1719 called it Los Inocentes. The name San Marcos was clearly the most common one applied to the river, however, being used by both Fray Isidro Félix de Espinosa and Fray Antonio de San Buenaventura Olivares in 1709 and by Domingo Ramón in 1716. Archeologists have found evidence at the river associated with the Clovis culture, which suggests that the San Marcos River has been the site of human habitation for more than 10,000 years. When Spanish explorers began arriving in the area in the seventeenth century, they found Tonkawa Indians camping near the river. In 1808 the Spanish established a settlement of their own, called San Marcos de Neve, just downriver from the site of present San Marcos. The Spanish found the Tonkawa Indians in the area friendly, but frequent attacks by Comanche Indians forced them to abandon the San Marcos settlement in 1812.
Although much of the land in the area was included in grants made by the governments of Mexico and the Republic of Texas, settlement of the San Marcos valley was delayed until after the annexation of Texas to the United States. The present town of San Marcos was established in 1846. Prairie Lea, established in Caldwell County in 1848, was another early settlement on the San Marcos River. Edward C. Burleson constructed the first dam on the San Marcos in 1849, in order to power a mill. Other communities built along the river included Martindale in 1855, Riverside (later Fentress) in 1870, and Luling in 1874. Rising as it does from springs fed by the Edwards Aquifer, the San Marcos River provides a reliable flow of water and would probably be the last river in the area to run dry in the case of a severe drought. It is not indestructible, however. It suffered greatly as a result of poor sewage control in the 1940s and 1950s, and for a time swimming in the river was declared unsafe. With the improvement of water treatment and sewage facilities, the river recovered much of its former clarity, although many people believe that its pristine quality is tarnished beyond repair. In addition to the threat of pollution, the river is endangered by increasing water demands and the potential depletion of the aquifer. Several plant and animal species, such as Texas wild rice and the Texas salamander, are unique to the San Marcos River, and if the springs feeding the river ever do run dry, these species will be lost forever. Although the San Marcos provides opportunities for recreation, public access to the river is limited to a few parks because most of the riverside property is privately owned. In addition to the facilities at Aquarena Springs, the river is accessible at a city park in San Marcos and at Palmetto State Park near Luling.