San Juan County is in the Four Corners Region on the western slope of the Rockies in northwestern New Mexico. A big part of the Navajo Nation is here, as is a lot of oil and natural gas activity. There are some great badlands at Angel Peak National Recreation Area, just southeast of Bloomfield. The Aztec Ruins National Monument is inside the city limits of Aztec.

San Juan County contains 5,514 square miles of land and 24 square miles of water. The county seat is Aztec.