Sand Dune Pony is the story of a boy named Pete and a wild mustang pony set in what is now Great Sand Dunes National Park in Colorado. At the center of the story is a sinister individual who is seemingly dedicated to causing random harm. Pete and an old cowboy by the name of Hatsy get to the bottom of the mystery as they come across the remains of long-dead humans and the bodies of slain animals.

The recurrent themes of the books in the Wilderness Mystery Series are natural phenomena—caves, canyons, mountains, sand dunes, and forests—and a sense of the past as seen through archaeology. In many of the narratives, events of long ago are seen to have left traces of their passing. Notwithstanding the fact that the books were written in the 1950s, the progressive Franklin Folsom (alias Troy Nesbit) had refreshing views of women, Native Americans, and the environment, and he was prescient in having his characters often oppose corporate and government efforts to develop wilderness areas.