(Reuters) - The U.S. Environmental Protection Agency said on Thursday it reached an agreement with the U.S. Marine Corps to bring water systems at Camp Pendleton near San Diego up to code after the remains of small animals were found in the drinking water.

The agreement came three months after inspectors also found that the water treatment plant that serves 55,000 people on the base was not regularly inspected, tested and maintained, and that operators and supervisors were not qualified, the EPA said in a statement.

Inspections of the base’s two water systems in June found “several significant deficiencies”, including small animal remains in three water reservoirs, that the treatment plant was periodically shut down, and cracks in the foundation and inadequate seals, the EPA said.

“Public water systems must meet all state and federal requirements to provide safe drinking water to their customers,” Alexis Strauss, the EPA’s Acting Regional Administrator for the Pacific Southwest, said in a statement.

“Our priority is to ensure the base achieves compliance promptly, to serve those who live and work at Camp Pendleton.”

Inspectors found decomposed rats on a reservoir gate, a desiccated frog on a reservoir ladder and a rodent carcass floating in treated water, the San Diego Union-Tribune reported.

Marine Corps officials removed the animal remains and cleaned, refilled and tested the reservoirs for coliform bacteria and chlorine, used as a disinfectant, after the inspection. Officials will conduct additional testing to “ensure the water in the reservoirs is safe to drink,” the EPA said.

“Simply put, the water is and has been safe to drink. Camp Pendleton is committed to providing safe and compliant drinking water. This is a duty and responsibility that we take very seriously,” base spokesman Carl Redding said in a statement emailed to the newspaper.

The agreement requires the Marines to inform customers of ongoing compliance issues, test for coliform bacteria and clean all water reservoirs within 180 days.

If the water tests positive for coliform, the Marines must issue a public notice and provide affected customers the choice to receive an alternative source of drinking water, the EPA said.