The Magdalena Mountains are an east-tilted fault-block range, superimposed on Cenozoic calderas. They form part of the western edge of the Rio Grande Rift Valley, fronting the La Jencia Basin. Much mining activity, involving gold, silver, zinc and lead, occurred on the west side of the range between 1866 and 1960. The mines in the vicinity are particularly well known for museum-quality specimens of the zinc carbonate mineral Smithsonite.

Most of the Magdalena Mountains are within the Magdalena Ranger District of the Cibola National Forest, and parts are administered by the Bureau of Land Management. There are no designated wilderness areas in the range, but there are sizeable (up to approximately 35,000 acre) roadless areas featuring trails and abundant hiking opportunities. There are two Wilderness Study Areas in the southern end of the range. At the southern end of the main range crest, just south of South Baldy, lies the Langmuir Laboratory for Atmospheric Research of the New Mexico Institute of Mining and Technology (New Mexico Tech). The same area hosts the Magdalena Ridge Observatory Interferometer, also operated by New Mexico Tech, along with other institutions.

Significant summits include:

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