A stew of sewage and toxins that puts surfers and swimmers at risk of disease closed beaches north of the metal barrier dividing Tijuana, Mexico, from San Diego for more than 80 days last year.

Special Report

Pollution flowing north from Mexico in the Tijuana River could worsen. Eroded earth is smothering plant life and destroying the fragile Tijuana Estuary, one of California's last salt marshes and an important filter for water flowing into the Pacific Ocean.

Eroded sediment, primarily from development on Tijuana hillsides, already has destroyed 20 acres of the estuary. And environmental groups say it's being further imperiled by federal plans to complete three-plus miles of double border fencing beginning at the ocean.

The problem is that the fencing project includes removing a 150-foot-wide strip of vegetation to make room for a patrol road between the walls. Vegetation prevents sediment from tumbling down the hills along the border into the 2,500-acre Tijuana River National Estuarine Research Reserve. Sediment and the non-native seeds it brings with it chokes the estuary's plant life. Adding earth to the estuary also can cause elevation to change, turning a salt marsh into dry land.

More such fencing along the international line would threaten wildlife habitat, biological diversity, recreation areas and federally protected land, some environmentalists say.

The construction of fences -- and the roads needed to build them -- denudes huge swaths of land and affects the migratory patterns of jaguars, wolves, bobcats and other animals. Improperly built fences can damage ecosystems with erosion, too.

People also could be affected. Ocean pollution has hampered the surfing business and area tourism, says Ben McCue, coastal conservation program manager for Wildcoast, a nonprofit group of mostly surfers based in Imperial Beach that aims to preserve coastal ecosystems. Contaminants in the ocean put swimmers and surfers at risk for hepatitis, ear infections and gastrointestinal problems, he says.

Though Wildcoast says existing plans for the new border fence don't ensure water quality, the government counters that the fence will more than make up for the loss of habitat that would occur with an unsecured border. Federal officials also say they're minimizing damage to plant and animal life.

"Having personally seen traffic where thousands are coming across at any given time -- at our height 500,000 a year were coming across -- if you can stem foot traffic, you can protect much more environment than you would affect," said James Jacques, a spokesman in the U.S. Border Patrol's San Diego sector.

But protecting the border environment is a complex balance.

In national lands and wildlife refuges on the border, illegal entrants leave piles of trash and human waste, and roads and trails are closed to the public because drug-smuggling traffic has created a safety hazard.

And areas like the 118,000-acre Buenos Aires National Wildlife Refuge in Arizona -- once a peaceful spot for bird watchers -- have turned into war zones where helicopters buzz in the sky, National Guard troops patrol and Department of Homeland Security buses wait for new loads of illegal entrants.

Public lands are also threatened west of Buenos Aires; Organ Pipe National Monument has closed one-third of its 331,000 acres because of public-safety concerns.

Still, foot traffic has led to a major problem in federally protected areas along the border: garbage. Crossers have left behind hundreds of thousands of pounds of it, from clothes and old food cans to feces, graffiti and old cars.

"I support trying to have security here without a wall. But if that can't be done using all possible methods … well then, maybe the next step might be a wall," said Roger Di Rosa, manager of the 860,000-acre Cabeza Prieta National Wildlife Refuge. "If you put in a wall, yes, you are going to affect the ecology as far as the interchange of species. But, you are also protecting a lot of habitat behind it and increasing border security at the same time."

Environmentalists fighting border security are not taking the issue seriously enough, says Ira Mehlman, spokesman for the Federation for American Immigration Reform, a nonprofit group that supports improved border security.

"They don't seem to be worried about literally millions of people coming through and trampling flora and leaving tons of trash out there," he said.

The defense of America ought to trump what in the great scheme of things are small environmental concerns, concurs Steven Camarota, director of research at the Center for Immigration Studies, which favors a wall as part of border-enforcement strategy. The U.S. population is swelling because of illegal immigration, Camarota says, and that will cause pollution and sprawl.

Though federal officials say they've completed necessary environmental studies to proceed with the project and are taking care to ensure minimal disruption of wildlife habitat, environmentalists maintain the plan imperils the Tijuana Estuary.

Further aggravating to many people committed to protecting land and animal species along the border was the passage of federal legislation in 2005 that allows the Department of Homeland Security to skirt all laws, even the Clean Water Act and the National Environmental Policy Act, in the name of national security. The legislation came under the Real I.D. Act, which was tacked onto an $82 billion spending bill for U.S. troops in Iraq.

Homeland Security Secretary Michael Chertoff named the Real I.D. Act last fall when he announced he'd be expediting the San Diego fence project.

The nearby estuary is one of 22 wetlands in the U.S. the United Nations considers internationally significant. It includes five species of endangered birds and is more biologically significant and diverse than the redwood forest, says Clay Phillips, who manages the estuary's research reserve.

If Congress must build fences, it needs to make sure the projects are properly executed and researched, and not just short-term fixes, says Jim Peugh, conservation committee chairman of the San Diego Audubon Society, whose group filed an unsuccessful lawsuit over the San Diego double-fence project. The case was dismissed because of the Real I.D. Act.

"The sad thing is, we could go ahead and seal the border, and then some year not long from now we may not want any border protection at all. But by then, it's going to be too late."