The peaks and mountain ranges are primarily Paleozoic and Jurassic basement rocks, which consist of marble, schist, and gneiss.

The marine incursion of the ancestral Gulf of California also introduced a single, very large depositional system (the Colorado River delta) into the Salton Trough, which rapidly prograded to the south (Winker and Kidwell, 1986).

The Deguyños Formation represents the distal prodelta portion of the Colorado River delta, and is characterized by upward-coarsening cycles of claystone, siltstone, sandstone and/or coquina shell beds.

In the Coyote Mountains, this is expressed by the presence of upward fining sequences of fine, light pink to pale orange sandstones and reddish-gray mudstones, known as the Arroyo Diablo Formation of the Palm Spring Group (previously the Diablo member of the Palm Spring Formation).

[12] Further deposition of locally derived sediments continued to accumulate in the area between 2.8 and ≈1 million years ago, primarily manifested by the Hueso Formation.

The Salton Trough itself is a pull-apart basin that is the result of crustal stretching and sinking by the combined actions of the San Andreas Fault and the East Pacific Rise.

Wind and rain carve steep canyons into the recently exposed rocks, and transport loose material downslope.

Gravels derived from this erosion form terraces as old as the Pleistocene and as recent as the Holocene (current epoch), which overlie all of the units in the Coyote Mountains.

On the north side of the Coyote Mountains, these drainages carve into the poorly lithified sediments of the Imperial and Palm Spring Groups, forming the Carrizo Badlands.

Sediments of the Imperial and Palm Spring Groups north of the Coyote Mountains are deformed by the recent uplift of the range.

Brittle and ductile deformation of sediments in this area is consistent with prior interpretations of uplift and inversion of the Fish Creek–Vallecito basin as a result of initiation of the Elsinore and other strike-slip faults in the western Salton Trough ≈1.2 Ma (Dorsey et al., 2011).