Some parts of the wilderness area rise quickly from sea level, reaching a peak of just over 3,500 feet (1,100 m) at the summit of Otay Mountain.

[8] The public lands within the Otay Mountain Wilderness are one of the last remaining pristine locations in western San Diego County.

[4]: 11–12] Species of special concern on Otay Mountain include:[10] In the mid 1990s, as part of Operation Gatekeeper,[13] Department of Homeland Security contractors began to build a border wall,[14] and associated access roads.

Grading and construction of roads in the wilderness area would result in removal of layers of topsoil and delicate, intertwined root systems that protect dry chaparral habitat from erosion.

[17] In December 2008 work began to continue the wall's progress through the wilderness area,[17] under the auspices of the Secure Fence Act of 2006.