The San Marcos River rises from the San Marcos Springs, the location of the Meadows Center for Water and the Environment, in San Marcos, Texas. The springs are home to several threatened or endangered species, including the Texas blind salamander, fountain darter, and Texas wild rice. The river is a popular recreational area, and is frequented for tubing, canoeing, swimming, and fishing.

San Marcos Springs is the second largest natural cluster of springs in Texas. The springs are located in the city of San Marcos, Texas, about 30 miles (48 km) southwest of Austin and 46 miles (74 km) northeast of San Antonio.