San Juan takes its name from the San Juan River, whose headwaters are in the nearby San Juan Mountains. Once home to the Anasazi, the prehistoric people's ancient pueblo ruins are preserved at Aztec Ruins National Monument, located in Aztec, the county seat.
The county also contains large parts of Chaco Canyon National Historical Park and the Navajo Nation.
Agriculture has traditionally been an important part of the local economy, as implied by the name of its largest city, Farmington. Energy rich, San Juan has in recent years experienced the development of oil, gas and coal resources.