The Environmental Restoration Program is responsible for carrying out the cleanup actions outlined in the past 25 records of decision under the Federal Facility Agreement and Consent Order. The program also ensures institutional controls (such as monitoring, fencing, and other environmental protection measures) are carried out while the DOE's Idaho National Laboratory Site remains on the National Priorities List of Superfund Sites. After cleanup actions are complete, the program conducts five-year reviews to ensure protective measures are still effective. The program can also launch environmental investigations of potentially new, previously unidentified sites to properly assess whether those sites pose an unacceptable risk to people or the environment.

A large part of the Environmental Restoration Program's responsibilities is the protection of the Snake River Plain Aquifer. An active groundwater treatment system is in operation near the former Test Area North where a pump-and-treat system removes contaminants from the aquifer, while another project introduces food-grade whey into the aquifer to encourage microorganisms to "feed" on the solvent constituents present in the groundwater. Additional aquifer-protection measures are currently in place at other facilities or will be implemented in the coming years.

Every five years the Environmental Restoration Program conducts a detailed review of all previous comprehensive records of decisions to ensure the cleanup decisions remain protective of people and the environment. The current five-year review was completed in 2021.

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