The area surrounding the headwaters of the San Marcos River is a portal into Texas history.  Archaeological discoveries of Clovis points and Mastodon bones indicate that this area has been inhabited over 12,000 years. The Tonkawa Indians were one of the earliest native Americans to live in the area, followed by the Apache and Commanche Indians.  The first recorded history of non-Indian habitation was when the Spanish explorers found the bubbling springs over three centuries ago. Fransican Monks looking for areas to establish their missions came upon the river on  St. Mark's Day, thus naming the waters the San Marcos river.

One of the founders of the city of San Marcos, General Edward G. Burleson, built his home on the grounds at Aquarena Center in 1848 and later built a dam to run his Gristmill in 1851 creating Spring lake and covering up 12,000 years of artifacts.

Another early settler in San Marcos was Arthur B. Rogers, who built the Aquarena Inn, in 1928, then known as the Spring Lake Hotel and today the Texas Rivers Center. In 1946 Mr. Roger's son, Paul, initiated the beginning of Aquarena Springs by launching the first Glass bottom Boat. This was in the form of an over-sized, canvas-topped rowboat equipped with a small glass panel in the bottom. The Glass Bottom Boats were followed in 1951 with the first Submarine Underwater Theatre. In 1969 "Ralph" the famous swimming pig took his first swine dive.

Texas State University-San Marcos, then Southwest Texas State University purchased Aquarena in 1994, changing the focus of the former theme park, from entertainment to preservation and education. The 90-acre acquisition has enabled Texas State to preserve the beautiful, ecologically fragile site for the state, while opening up classroom, lab and research possibilities for the university.