During the 1980s, much attention was given to environmental issues both nationwide and on Cape Cod. Groundwater contamination was first discovered flowing off the southern portion of JBCC. The groundwater plumes emanated from areas of previous activity, mainly associated with those conducted at the former Otis Air Force Base (now Otis Air National Guard Base). The discovery of significant off-base contamination led to increased community interest in the existing environmental cleanup program at JBCC, now the Air Force Civil Engineer Center's Installation Restoration Program (IRP). As interest and activity grew in the IRP, the citizens and local community organizations began to look at other activities taking place at JBCC and voiced concern over potential contamination in the northern 15,000 acres of JBCC. The National Guard Bureau had begun its investigation and cleanup in 1996, which was soon followed by the Environmental Protection Agency (EPA) issuance of the first of four Administrative Orders in 1997.

In February of 1997, the Environmental Protection Agency utilized its powers under the Safe Drinking Water Act to issue the first Administrative Order concerning Camp Edwards. Administrative Order No. 1 (AO1) was issued to the National Guard Bureau (NGB) and it required the NGB to investigate the nature and extent of contamination at and emanating from the training ranges and Impact Area on Camp Edwards. AO1 also required that Groundwater Study Program activities be conducted with adequate public involvement, including establishing and supporting a citizen advisory committee to work closely with the EPA, the Massachusetts Department of Environmental Protection (MassDEP), the Groundwater Study Program and other agencies and community members. This team is now known as the Joint Base Cape Cod Cleanup Team.

The second Administrative Order No. 2 (AO2) was issued in April of 1997 to the National Guard Bureau and the Massachusetts National Guard. It required that certain training activities (artillery and mortar firing) cease pending the completion of environmental investigations at the training ranges and Impact Area. As of this writing, in 2003, these activities are still barred at JBCC.

In January of 2000, EPA issued Administrative Order No. 3 (AO3), which required the National Guard Bureau and the Massachusetts National Guard to conduct rapid response actions, feasibility studies and remedial actions to address contamination in certain areas of the training ranges and Impact Area. It required the NGB to undertake a feasibility study to address unexploded ordnance (UXO) and munitions, which have been disposed of or fired at the training ranges and Impact Area. It also required the NGB, upon approval from EPA, to implement remedial measures relating to UXO and munitions.

Administrative Order No. 4 (AO4) was issued on January 4, 2001 under the Resource Conservation and Recovery Act (RCRA) to the National Guard Bureau. This order requires that munitions found subsurface or in burial pits be properly stored and disposed of in a Contained Detonation Chamber (CDC), or by other means which prevent the release of explosives, metals and other contaminants into the environment.