The Environmental Program is a major part of the total Alaska District workload with three areas of emphasis: Formerly Used Defense Sites, Native American Lands Environmental Mitigation Program, and Army and Air Force Environmental Programs. Other environmental programs are performed under Interagency and International Services.

Under the Defense Environmental Restoration Program, the district has identified more than 500 sites that are eligible for the Formerly Used Defense Sites program in Alaska. The environmental cleanup under this program is estimated to continue beyond 2020 with nearly $1.2 billion worth of cleanup work yet to be completed. Additionally, the district executes environmental projects on behalf of the Army and Air Force at installations across the state.

The district manages the Native American Lands Environmental Mitigation Program (NALEMP) for the entire state. Under NALEMP, the district enters into cooperative agreements with federally-recognized tribes whose lands have been impacted by past military activity. Under these agreements, the district assists the tribes in mitigating environmental impacts using tribal resources instead of contractors. With more than 600 former military sites and 229 tribes, many impacts need to be handled in Alaska. The district has about 30 active cooperative agreements.

The Alaska District is providing technical support to the Army and Air Force throughout Alaska in support of Defense Environmental Restoration Program (DERP), the Compliance-related Cleanup Program and the Compliance Program.

The DERP was formally established by Congress in 1986 and consists of the Installation Restoration Program (IRP) and the Military Munitions Response Program (MMRP). The IRP is a comprehensive program to identify, investigate and clean up hazardous substances, pollutants and contaminants at active installations. The MMRP deals with nonoperational range lands that are suspected or known to contain unexploded ordnance, discarded military munitions or munitions constituent contamination.

The Compliance-related Cleanup Program refers to the cleanup of contamination resulting from operations occurring since October 1986, which are ineligible for DERP. The Compliance Program involves air, water and waste media areas.