This dark reddish-brown slender salamander reaches lengths of one to two inches, and has moderately large eyes with a dark ring around the lens. The species has well developed and highly pigmented gills, relatively short, slender limbs with four toes on the fore feet and five on the hind feet. San Marcos salamanders have a slender tail with a well-developed dorsal fin.

Historically it was unclear whether the population of salamanders at the headwater of Comal Springs could also be San Marcos salamanders, but the best available genetic information indicates that the salamanders at Comal Springs are Eurycea pterophila. Genetic information previously suggested that salamanders found at springs in northern Hays County could be San Marcos salamanders. However, more recent studies with additional genetic information determined that the salamanders at the springs in northern Hays County are Barton Springs salamanders, Eurycea sosorum.

Reproduction occurs throughout the year. Courtship and eggs have not been observed in the wild, and may possibly be restricted to subsurface habitat. San Marcos salamanders do not go through metamorphosis into a terrestrial form.  Instead, they retain external gills and remain aquatic throughout their lives.

San Marcos salamanders are found in areas that contain cobble, gravel and boulder substrates, and may have coverage from Amblystegium moss or filamentous algae. Salamanders are less likely to be found in areas that have mud or silt substrates and rooted macrophytes, and are adapted to thermally stable spring environments. San Marcos salamanders prefer velocities around one centimeter per second. High velocities can wash away potential habitat while low velocities allow sediment to settle into the interstitial spaces that they use as habitat. The difficulty of access for subterranean habitats makes determining subsurface habitat characteristics difficult.

San Marcos salamanders prey on a variety of macroinvertebrates, including amphipods, midge fly larvae and pupae, other small insect pupae and naiads, which are an aquatic life stage of mayflies, dragonflies, damselflies and stone flies. They are also known to eat small aquatic snails.