The former Castle Air Force Base, like numerous military installations across the country, was contaminated by fuels, oils, solvents, cleaners and paints used to operate and maintain aircraft for national defense. Federal laws such as CERCLA (the Comprehensive Environmental Response, Compensation and Liability Act) require the Air Force, overseen by state and federal regulators, to clean up this soil and groundwater pollution, a task which is almost finished.

All cleanup decisions have been made; all necessary equipment has been installed and is operating properly and successfully. Some cleanup equipment has completed its task and been dismantled. Thousands of pounds of contaminants have been removed from the soil and groundwater. Where groundwater cleanup or site operations and maintenance is ongoing, the Air Force has implemented restrictions to protect human health and the environment.

Groundwater contamination was initially discovered at Castle Air Force Base in 1979, well before the base closed in 1995. In response, the Air Force conducted investigations, constructed new base water supply wells, and connected residents on the base boundary to the new water supply. Continued investigations revealed more widespread contamination issues involving trichloroethylene (TCE), a solvent used to remove grease from metal parts; 1,2-dichloroethylene (1,2 DCE), a solvent used in painting lacquers; and various jet fuels. Throughout the investigation and cleanup period, a safe drinking water supply has always been and continues to be provided at Castle. The Air Force has ensured safe drinking water on the former base and for surrounding off-base residents by continued monitoring and by providing treatment or replacement of water supply wells, where appropriate.

The Air Force started operating three small groundwater treatment systems between 1991 and 1996 that treated over 1.7 million gallons and removed approximately 1,054 pounds of solvent contaminants. In 1994, operation of OU 1, the first of three groundwater treatment plants to address basewide groundwater contamination, was started at Castle to replace one of these small systems. Water was pumped in from five different extraction wells, then treated by pumping it into the top of an air-stripping tower while air was blown into the bottom, stripping volatile contaminants out. Cleaned water was then injected back into the ground. The air used in the stripping process was filtered through carbon to clean it.

The OU 1 plant treated the highest levels of groundwater contamination, what was then a so-called "hot spot," an area that initially contained 500-700 parts per billion of contamination. (For contrast, the highest contaminant levels anywhere on the former base are 21 parts per billion as of 2018.) The OU 1 system was turned off in 2003 with regulatory approval after it had completed its primary role of removing contamination from the "hot spot." The OU 1 system treated over 1.6 billion gallons of groundwater and removed approximately 700 pounds of contaminants (the primary contaminant removed by all base groundwater systems is the cleaning solvent TCE.) The OU 1 system was decommissioned in 2011, although the equipment pad and building were retained and transferred to the County of Merced for reuse.

A second groundwater treatment plant, known as OU 2, started operating in 1996 to treat contaminant source areas on the west side of the base near Wallace Road and portions of the contaminant plume that had migrated off base. The OU 2 system replaced two smaller systems that had been installed in the early 1990s. Rather than using an air stripper as at OU 1, this system used carbon filtration, pumping water through up to three pairs of vessels containing activated charcoal. Each vessel contained 20,000 pounds of activated carbon, which absorbed the groundwater contamination and needed to be replaced about every six months. As of December 2018, the system has been reduced to one pair of vessels each containing 2,000 pounds of activated carbon.  Through December 2018, the OU 2 system treated over 5.6 billion gallons and removed approximately 875 pounds of contamination. The OU 2 system has reduced the size of the groundwater contamination area to the point where as of December 2018 it is necessary to operate only four  of the original 15 extraction wells to address the remaining contamination.

The third water treatment plant installed to address basewide groundwater contamination at the former Castle AFB is known as Phase 3 and was built in 1997. The plant featured an air-stripping tower and three pairs of carbon filters similar to those used at OU 2. In its heyday, the plant treated 2,200 gallons of water a minute; as of December 2018, the size of the plume was reduced so that only 700 gallons per minute were being treated. Throughout Castle, the size of contaminated groundwater plumes continues shrinking, as do the concentrations of the TCE and other contaminants. Through December 2018, the Phase 3 system treated 8.7 billion  gallons of groundwater and removed approximately 1,308 pounds of contamination.

Considering all groundwater systems at Castle, a total of 15.9 billion gallons of water has been treated and 3,937 pounds of contamination removed. Groundwater cleanup and monitoring will continue until health-protective levels are achieved throughout the groundwater contamination area.

In addition, the Air Force used Soil Vapor Extraction (SVE) at 22 sites, mostly to remove TCE and jet fuel present in the soil as a result of historical releases. Over 1,000 pounds of TCE contamination and over 25,000 gallons of fuel contamination was removed from the soil. All SVE systems have been turned off and the regulatory agencies have agreed that no further action is required.

There were seven landfills used for waste disposal at the former base. The Air Force consolidated these into two landfills, one of which is 18 acres and the other, 12 acres. These are capped to prevent rainwater percolating through them into the groundwater. The landfills are vented to prevent methane buildup. Monitoring wells in the vicinity ensure methane or contaminants from the landfills do not migrate to adjacent property or leach into groundwater. In accordance with state and federal regulations, the landfills will be maintained and monitored for at least 30 years.