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Environmentalists call it a disaster. The government says it's a matter of national security. The Department of Homeland Security is building more than 600 miles of fence along the southern border with Mexico. And as part of the project, contractors have been working in a canyon that runs between Tijuana and San Diego. It is a notorious smuggling route into the U.S., known as Smuggler's Gulch, and workers have filled it with almost 2 million cubic yards of dirt.

NPR's Jason Beaubien went to take a look.

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Mr. JIM PEUGH (San Diego Audubon Society): We're in the bottom of Smuggler's Gulch, which is about, oh, I guess about two miles in from the ocean right along the border.

JASON BEAUBIEN: Jim Peugh is with the San Diego Audubon Society, which has vigorously opposed this project.

Mr. PEUGH: Right in front of us, we're seeing a berm that was just built in the last, you know, six months.

JASON BEAUBIEN: Bulldozers march up and down the steep slopes of what looks like a huge, earthen dam.

Mr. PEUGH: And it's filling in, it crosses Smuggler's Gulch, which is about half a mile across. The berm is something like 180 feet high by about 800 feet wide.

JASON BEAUBIEN: When the berm is finished, a Border Patrol road will run across on top of it. At night, stadium lights will flood the area. And instead of one rickety old barrier, there'll be three new lines of fence.

Smuggler's Gulch got its name decades ago, as every type of contraband imaginable, from cattle to moonshine to cocaine, flowed through here. In the 1990s, this rugged canyon became symbol of an out-of-control border. Nightly, dozens of illegal immigrants would duck in and out of the steep slopes to skirt past a few, outnumbered Border Patrol agents.

Peugh, with the Audubon Society, acknowledges that the government faced huge challenges in patrolling Smuggler's Gulch. But he says filling it with dirt was overkill.

Mr. PEUGH: The big threat to the environment that I see is the erosion from that berm, and from the slopes that they've cut to borrow soil for that berm.

JASON BEAUBIEN: This project was originally proposed 12 years ago. Opponents held it up for years. Eventually, the Bush administration granted the Department of Homeland Security authority to override all local and environmental regulations to move forward with building the border fence.

Mike Fisher is the chief Border Patrol agent for San Diego. He says, historically, Smuggler's Gulch has been a major problem for his agency.

Agent MIKE FISHER (Border Patrol) We did not have easy access into that area, nor do we have easy access across that gulch. As a matter of fact, unfortunately, we lost a Border Patrol agent in that area on patrol one night because of the rough terrain. And the smugglers were exploiting that vulnerability.

JASON BEAUBIEN: Despite the waiver of environmental regulations, Fisher says environmental concerns are being addressed at the berm. A huge culvert is being installed, and the slopes are being reseeded for erosion control.

In addition to the new triple fencing, the federal government is also deploying remote sensors, new cameras, and hundreds of additional officers along this section of the border. Many human smugglers have given up trying to cross here, and moved to remote parts of the Arizona desert.

But Fisher says the threats here remain real.

Agent FISHER: Every day, there are people who wake up and think about nothing else than to do harm to this country. We're talking about narcotics smugglers. We're talking about potential terrorists, whether they be operatives, financiers or facilitators. And our job, that one of border security, is as real, and those threats are as real, today as they were five years ago.

JASON BEAUBIEN: The filling of Smuggler's Gulch is part of a $60 million project to install triple fencing along the final 3.5 miles of the San Diego-Tijuana border. The new barrier will extend all the way into the Pacific, and it's changing the landscape of the border.

Mike McCoy started lobbying to get this area set aside as a wildlife refuge back in 1971. Looking out over an expanse of bulldozed earth and half-finished fence at Smuggler's Gulch, McCoy says this project is destroying a fragile coastal ecosystem.

Mr. MIKE MCCOY (Southwest Wetlands Interpretive Association): At first, I didn't want to come back here again. But now I sort of, I come back, but I don't really see it the same as it was.

JASON BEAUBIEN: McCoy has worked for decades to clean up and restore the Tijuana River estuary.

Mr. MCCOY: We're seeing a lot of erosion right here, right in front of you there. And that adds up to disaster when you start transporting that down into a river system.

JASON BEAUBIEN: The river carries sediment to the estuary, and if that tidal coastal zone fills with sediment, he says native plants and animals won't be able to survive.

McCoy seems most irked at the heavy-handedness of the federal government in overriding all environmental rules to push forward with the fortification of the border. The Department of Homeland Security argued that those rules could have blocked the new fence indefinitely.

Jason Beaubien, NPR News. Transcript provided by NPR, Copyright NPR.