Camp Navajo was first established as the Navajo Ordnance Depot in 1942 for support of wartime efforts in the Pacific Theatre. Its mission included the storage, maintenance, and disposal of ammunition and other strategic war supplies, along with soldier training and other support activities. The Depot employed more than 2,000 people during World War II, and was the largest employer in Flagstaff and Coconino County at the time. In 1982, operational control was transferred from the Department of the Army to the Arizona Army National Guard (AZARNG). In 1988, Congress determined that the Army storage mission was no longer required, and the installation was slated for realignment under the Base Realignment and Closure (BRAC) Act. In 1993, the Army storage mission ended, the AZARNG was granted a license for an indefinite period of time, and the name was changed to Camp Navajo. Since 1993, the primary mission of Camp Navajo has been to provide a training site for National Guard, Reserve, and other units.

The RCWM Area on Camp Navajo known as Chemical Canyon is an area used to burn and vent CWM munitions in the 1950s as well white phosphorus (WP) and plasticized white phosphorus (PWP).

The RCWM area associated with Camp Navajo is an area known as AREE-3 (Chemical Canyon) that was used to burn leaking CWM munitions including mustard filled bombs back in the 1950s. The exact final disposition of the burned CWM bombs is unknown. The area was used for the venting of 500- and 1000-pound aerial bombs filled with cyanogen chloride and phosgene during a period of six to eight months in the early 1950s. A Drum Burial Site, formerly designated as NAAD 44, is also located here.