CAMP PENDLETON -- Camp Pendleton's 50-year-old wastewater system has been spewing raw sewage into the Santa Margarita River Basin at alarming rates for years, violating the top federal clean water laws without penalty.

But new federal funding and a tighter grip on the management of the system may stem the foul flow and put an end to the toxic spills over the next seven years.

Hidden within the $401 billion defense authorization act recently signed by President Bush was a tiny provision approving $25 million for the first phase of construction of a tertiary sewage plant planned for the southwestern corner of the 125,000-acre Marine Corps base.

Having a tertiary plant means the wastewater, or effluent, will be treated to a level of purity that means it can be reused throughout the base to water lawns, wash cars and irrigate the golf course.

The one tertiary plant will replace the existing four outdated and faulty secondary plants that only remove the bulk of the solids from the waste and continue to pump treated water into the river basin that does not comply with federal Clean Water Act standards.

"It's a good thing for the base and it's a good thing for the environment," said Steve Wolfe, deputy public works officer for Camp Pendleton. "The results will be so much better than what we have now."

The first $25 million on the Pentagon budget this year is only starters.

Another $25 million will have to be approved on next year's defense spending legislation, as will an additional $50 million over the next six years for pipes and pumping stations. Planners estimate the system will cost about $100 million by the time it's finished in 2010.

Ending a practice

Under the current proposal, 100 percent -- about 3.8 million gallons a day -- of Camp Pendleton's wastewater will be treated and reused on base, ending the practice of dumping secondary sewage into the Santa Margarita River, a practice that has existed since the base was built during World War II.

"There will be a lot less bad stuff coming out of the plant," Wolfe said. He said a significant bonus is that the base will no longer use potable water for irrigation, resulting in a net gain for the aquifer and health of the ecosystem.

Until a system is built to distribute the treated water back to "reuse" sites around base -- which is the last phase of the project -- the remainder of the effluent will be routed to the city of Oceanside's "outfall" that pumps water into the ocean 1.8 miles off Buccaneer Beach on the south end of town.

In 2001, the military completed a $6 million, 2.2 mile-long pipeline linking the base sewage system to Oceanside's ocean-bound outfall. Based on a five-year agreement with the city of Oceanside, treated waste from Camp Pendleton started flowing through the Oceanside outfall in September.

A sordid record

Base officials and environmentalists agree that the prospect of a new sewage plant is good news. It came only after years of bad news; Camp Pendleton has a sad and sordid record of sewage spills.

In February, for example, nearly 110,000 gallons of raw waste poured into the base boat basin, an embarrassing spill that was apparently caused by an accumulation of grease in military housing drains and exacerbated by recent rains that overwhelmed the system.

Although spills had decreased last year and the February spill was seen as an unfortunate anomaly, it was really nothing new.

The California Water Quality Control Board has recorded at least 14,000 violations of state and federal clean water laws at the base since 1997.

In 2001 and 2002, Camp Pendleton alone dumped more than 3 million gallons of raw sewage into the Santa Margarita River.

While cities can and are fined huge sums for the same violations, federal facilities like Camp Pendleton and Miramar Marine Corps Air Station to the south are exempt. The two bases have been the worst polluters in the county, according to the California Water Quality Control Board.

Local efforts to get the government to clean up after itself hadn't worked until a recent lawsuit brought by environmental heavyweights forced the military to the table.

After the base failed to comply with an order to "cease and desist" pumping secondary wastewater into the river in 1999, the City of Oceanside gave them five more years to cut the flow.

Waiting for Congress

Nothing was done because the base needed Congress to approve the system improvements in the annual defense construction bill and fund them in the defense authorization bill.

In March 2002, however, a coalition of environmental groups filed suit, charging the base with several blatant violations of federal laws committed before 1990.

San Diego Baykeeper, the Surfrider Foundation, American Canoe Association and the Divers' Environmental Conservation Organization sued in U.S. District Court, forcing the military to settle in May of this year.

The settlement, which both sides say provides for a peaceful and appropriate solution to wastewater woes, includes base officials spending $5 million on replacement parts, streamlining management, improving monitoring and reporting, and launching an education program aimed at training the nearly 70,000 military residents and workers what to flush and dump down their drains.

It's a cooperative

While the most recent congressional action funding the base came only after the lawsuit, Wolfe said the base was pushing for federal funding for years.

"We've been on this track since 1999," he said. "When we were sued, we all sat down in a good spirit of cooperation. Their interest is to make sure we stay on track. We would not have approached this with any less vigor had we not been sued."

Cory Briggs, Baykeeper's lead attorney in the suit, said the base has to date done an excellent job of complying.

He said the environmentalists are staying out of the design and draft phase of the project but will reassert themselves into the process when it comes time to start construction.

The executive summary of the plant development proposal includes several alternative plans, including adding wetlands to filter some of the secondary water through reverse osmosis instead of the sewage plant.

One option, called a "no-action" proposal, maintains the status quo and allows for all the secondary treated water to use the Oceanside outflow. An expiration of the agreement with the city of Oceanside would result in secondary effluent that does not meet Clean Water Act standards continuing to be pumped into the Santa Margarita River.

The Navy is busy studying the possible environmental impact of the proposed plant and preparing the next draft according to standards set by the National Environmental Policy Act, officials said.

After the public and the environmental groups involved in the lawsuit have reviewed the final draft plan during a public hearing period in late March or early April, the project will be submitted to the assistant secretary of the Navy for facilities before it can go to bid.

The final Navy decision on the project -- called a record of decision -- is due June 4, at which time the litigants and the military will negotiate a time line for completion of design and engineering contracts and actual construction.

Woolfe said contracts could be awarded by September.

Contact staff writer Darrin Mortenson at (760) 740-5442 or dmortenson@nctimes.com.