The El Capitan deposit is located within a north-south-trending belt approximately 2 miles in width and 10 miles in area which is underlain by Permian limestone and lesser quartz sandstone. These sedimentary rocks crop out intermittently between the bold outcrops of the Miocene Capitan aplite intrusion to the east and rhyolitic volcanics and lesser interbedded basaltic volcanics and conglomerate to the west. The rhyolites are dominantly ash-flows and appear to be the extrusive equivalents of the aplite intrusion. Both the aplite and the rhyolites are unusually iron-rich; disseminations of limonite/goethite (original hematite) occur to some extent in most outcrops of these rocks. It is possible that the iron-rich composition of these rocks reflects crystallization from magmas that originated by differentiation from mafic/ultramafic magmas at depth; as noted above, coincident aeromagnetic and gravity anomalies in the region suggest deep mafic/ultramafic compositions.

The El Capitan deposit is exposed in a shallow open pit and outcrops within a nearly circular area 1,300 feet in diameter. Smaller bodies of mineralization similar to that in the deposit stretch up to 1 mile to the east-southeast and have been located up to 1 mile to the west-southwest of the deposit. Kelly (1952) attributed the circular shape of the main El Capitan deposit to a solution collapse structure in the host San Andres limestone of Permian age. Drill results indicate, however, that the deposit extends in all directions beyond the area of surface exposure and that the circular shape is simply an erosional expression of a shallow-dipping skarn deposit.

Cross-sections show that the overall form of the El Capitan deposit is that of a flat-lying to shallow west-dipping body of skarn surrounded by crystalline limestone lying on the aplite intrusive contact. Interbeds of quartz sandstone interrupt the continuity of the skarn and crystalline limestone. The mineralized body is at least 3,000 feet long in an east-west direction, at least 2,000 feet wide north-south, and ranges in thickness up to 400 feet in depth. Although potentially economic gold-platinum assays are concentrated in the skarn and crystalline limestone, potentially economic grades occur in all rock types, including fractured, stockworked, or brecciated quartz sandstone, limestone, and aplite.

The El Capitan skarn includes two magnetite-dominant zones (upper and lower magnetite bodies). The upper magnetite zone lies below a limestone cap that is bleached, fractured, and contains hematite-calcite fracture filling. This limestone cap is nowhere more than a few tens of feet thick and it passes up-section into fresh limestone. A variety of skarn assemblages including magnetite, hematite, calcite, phlogopite, diopside, quartz, tremolite, and crystalline limestone lie below the upper magnetite zone and limestone cap rock and above aplite of the Capitan pluton. At this stage, no zonal pattern has emerged among skarn facies. The aplite contact has a shallow westerly dip, ranging in depth, where drilled, from 100 feet in holes to the east to 450 feet in holes to the west.

The most striking characteristic of the El Capitan deposit is the ubiquitous and commonly abundant presence of hematite, oxidized to limonite or goethite on surface and in the upper parts of drill holes. Hematite occurs as a primary constituent in all skarn assemblages and as post-skarn fracture-fillings, stockworks, breccia- fillings, and replacements with calcite in skarn, limestone, sandstone, and aplite. Hematite commonly exceeds 12% and ranges as high as 80% in some drill intervals. Fracture-filling and replacement hematite-calcite clearly represent a later-stage hydrothermal event that was superimposed on earlier rock types. An assumption that these fluids were derived exclusively from the aplite is questionable because fracture-filling hematite-calcite occurs in aplite in the deeper parts of some drill holes. It is therefore apparent that at least some portion of the hematite-calcite hydrothermal fluids were derived from a deeper source underlying the aplite intersected in drill holes.

Precious metals in the deposit appear to correlate with the presence of hematite-calcite: higher gold-platinum values generally occur in both surface and drill samples with higher percentages of hematite. Samples dominant in magnetite, by contrast, are consistently lower in Au, Ag, and Pt. That precious metals correlate with hematite is supported by a study of two hematite-dominant samples from the El Capitan deposit conducted at the Missouri Bureau of Mines in 1996. Reflected-light microscopy and scanning-electron microscopy with energy dispersive spectroscopy (SEM-EDS) showed 2- to 35-micron crystals of electrum (Au-Ag alloy), native gold, and an unidentified possible Pt mineral. An apparently magnetite-dominant sample showed no Au, Ag, or Pt.