From its northern intersection with the Chesapeake Bay to its southern convergence with the Intercoastal Waterway, the Elizabeth River hums with commerce.

At the Norfolk Naval Station, sailors and intelligence officers are tweaking the nation's defense systems for one of the world's largest military bases. Just to the south, the Port of Virginia's Norfolk International Terminal moves billions of dollars of freight around the world. Farther south, the Norfolk Naval Shipyard and several private companies focus on shipbuilding. The world's largest coal export facility is nearby, as are refineries, loading docks, container-repair facilities and working barges.

All of that activity makes the estuary vital to the four Virginia cities - Norfolk, Chesapeake, Virginia Beach and Portsmouth - that ring it, and to the more than 500,000 people who live and work in its watershed. Yet over the years, it has given the Elizabeth the unhappy distinction of not just being one of the most polluted rivers in the Chesapeake Bay, but in the nation.

For decades, this urban river was not merely unloved, but unlovable. Who could feel good about a body of water that was a dumping ground for toxics from treating wood and sandblasting ships? Why focus on restoring a river that few could remember being anything but dirty?

But in 1991, the tide began to turn for the Elizabeth River. A group of concerned citizens gathered around a kitchen table, determined not to give up on the river that Jamestown colonists named for England's Princess Elizabeth Stuart. In 1993, the group incorporated as the Elizabeth River Project. Marjorie Mayfield Jackson, a Georgia native who had moved to the area to become a reporter for Norfolk's Virginian-Pilot, stepped up to run the new organization.

The job would require at least as much persistence as her newspaper career.

"People thought it was already dead, so why bother?" Jackson recalled on a recent afternoon trip along the water. "All these interests were at loggerheads. The environmental folks didn't talk to the businesspeople. Nobody would talk to anybody. And here we were, this brand-new environmental group. We decided we had to not point fingers, not talk about the past, but focus on the future."

That attitude has served the Elizabeth River Project well. In less than two decades, the 10-person group has led the charge to restore hundreds of acres of wetlands, removed thousands of tons of contaminated sediment and is in the process of turning a once-urban wasteland at Paradise Creek into a waterfront park with 11 acres of wetlands. They are also restoring four or five more acres elsewhere in the Paradise Creek watershed and building a 40,000-seed oyster reef.

In addition, the group has developed a program to certify businesses, schools and homeowners who are doing right by the environment through planting wetlands, treating stormwater from outfalls and creating wildlife habitats. So far, 84 businesses and 126 schools have received the project's Riverstar certification, while nearly 300 homeowners have signed up for the program.

"They get more done than any group I've ever seen," said Bill Cofer, president of the Virginia Pilot Association. As a Chesapeake Bay ship pilot, he has navigated freighters and container ships on the river for decades and has been involved with the cleanup through a sister organization, the Living River Restoration Trust. The Trust pays for the projects that the Elizabeth River Project has outlined in its plans.

They have accomplished those successes by focusing on one of the Chesapeake's most intractable problems - the goo and gunk at the bottom of industrial harbors. Contaminated sediment is the third leg of the Chesapeake's pollution stool, along with nitrogen and phosphorus, but it rarely gets much attention. In part that's because no one can see it; in part it's because cleaning it up is so expensive.

But Elizabeth River scientists and their partners at other Virginia universities have long argued that there was no point in doing any other restoration work until they get to the bottom of the problem. If they were to restore a wetland and not deal with the bottom contamination, the fish and crabs that they attracted would quickly die, because the animals at the bottom of the food chain couldn't support them.

To combat the problem, the project adopted a catchy phrase - The goo must go! - and found a powerful symbol in the mummichog. The small fish travels no more than 50 yards in its entire life and lives in direct contact with the river bottom.

In 2008, a Virginia Institute of Marine Science report showed that 38 percent of the mummichogs in the industrialized southern branch of the Elizabeth had cancerous lesions. More than half had pre-cancerous lesions. That was largely due to high levels of polycyclic aromatic hydrocarbon, or PAH, which came from now-abandoned wood-treatment facilities along the river.

That same year, the University of Maryland Center for Environmental Science's annual EcoCheck report card described the water quality as "consistently poor, showing no signs of improving."

Rather than throwing up their hands, the project's staff issued a challenge back to the community: Together, they would make the Elizabeth River swimmable and fishable by 2020.

A catchy slogan helped, but it was the mummichog that became the canary in the coalmine of the Elizabeth River restoration, and a powerful symbol of what needed to happen to bring the river back to life. The project settled on four sites with high levels of PAH - Money Point, Paradise Creek, Atlantic Wood Industries and Scuffletown.

The Money Point project was the first sediment cleanup project in the state. The bend in the Southern Branch of the Elizabeth, named because of the jobs and wealth created in the heyday of the river's factories, was a 35-acre biological dead zone in 2006 because of creosote contamination. Few thought anything could be done about it.

Then, a window opened. Maersk-APM, a major shipping company, wanted to develop a new port facility. Instead of objecting to the proposal, as other environmental groups might have, the project worked with regulators to secure $5 million in funding to restore the Money Point site as mitigation. That money went into the Living River Restoration Trust, which funded the cleanup.

Work began at Money Point in 2009, with earth movers lifting the first ceremonial batch of goo to an excited crowd of engineers, environmentalists and government officials. Since then, a pair of heavy orange jaws on a barge outside Money Point have taken out thousands of tons of contaminated sediment that was then transported to landfills. Meanwhile, the greening of Money Point continues. So far, the Elizabeth River Project staff has restored seven acres of wetlands, while the Hess refinery next door has voluntarily planted dozens of tulip poplars as part of a phyto-remediation initiative, which is using the trees to try to take up the polluted creosote and metals.

The work is already showing results, according to Josef Reiger, the Elizabeth River Project's senior scientist. Just one year after the first scoop of goo was gone, Rieger found nearly two dozen types of fish, shrimp and small crabs.

"People still say, 'there's not a lot of life left in it.' But we do surveys, and we catch up to 25 species. What we try to do is focus on those pockets that still remain," he said.

Sport-fishing has come back to the river, although the Elizabeth's shellfish have been off-limits since the 1920s because of pollution. Dave Koubsky, another project scientist who is also a fisherman, said someone on his boat caught a 42-inch striper about a year ago. The fish was migrating upriver to spawn.

Where Cofer remembers only concrete and lifelessness as he sailed Money Point's shores as a child, the area is lush and green today. Oyster beds have taken up residence in the once-toxic waters. And things are getting better; the City of Chesapeake recently received a grant for $370,000 worth of stormwater improvements on the site, which is home to a couple dozen residents and a Baptist church.

The rest of the money for the Money Point restoration will come from a federal and state requirement for the Virginia Port Authority, which is seeking to expand its port, to do mitigation. The port and its partners are expected to kick in $50 million for projects that are helping to clean up 67 contaminated acres.

"What we proposed - and what was ultimately agreed to - was that the port would clean up all toxics on the southern branch to replace what they were impacting," Jackson said.

Money Point is not the only green spot on the river. The Norfolk Naval Shipyard recently created a 70-acre wildlife area filled with meadows, wetlands and oyster floats. At the Scuffletown Creek project, which was mired for 17 years in a fight over who would clean it up, the Army Corps of Engineers has begun restoring 30,000 square feet of wetlands that are littered with construction debris.

Paradise Creek, once a dredge disposal site, is on its way to becoming an urban waterfront park. The Atlantic Wood Industries site, which became a Superfund site in 1990 because of creosote pollution, is now the site of another wetland where at least 18 species are living.

Asked how a small group with no regulatory power and few resources has been able to accomplish so much, Jackson said simply that it's the strength of partnerships. Or, as Pam Boatwright, manager of the group's Riverstar program, puts it: "We're not confrontational. We don't sue people."

Boatwright said peer pressure helps: No one, not even heavy industry, wants to be seen as a polluter. Only one business the project approached about a cleanup didn't want to participate, and in the end, regulations forced that business to clean up its mess anyway.

The Elizabeth River's fingerprints extend past the river, to partnerships with Norfolk's museums and cultural institutions. Thanks to its relationship with the Virginia Zoo in Norfolk, horticulturalist Marc Snyder has been restoring wetlands, planting rain gardens and replacing walkways with pervious pavement. Plants such as hibiscus and spartina seem to be as much of an attraction as the elephants and lions.

"Our partnership with the Elizabeth River is so important, for both of us," Snyder said. "You can come here to the zoo and learn directly about the environment, where the water goes."

The project has a long way to go before it can reach its goals. Yet, it has much to celebrate: 214 million pounds of pollution have been removed from the waterway, and more come out every day. With a trail around the river and new urban parks coming online, the river's name is no longer mud to the cities that ring it.

Other watershed cities, including Baltimore, are looking at the project's 16-year track record and wondering how to replicate its success. Recently, Reiger spoke to a conference organized by the Baltimore Waterfront Partnership, which also seeks to make that city's harbor swimmable and fishable by 2020.

Reiger's advice? Write a watershed plan, then follow it. Start at the bottom. Don't ignore the sediment, even if you can't see it, because if the smallest bottom-dwellers won't survive, then nothing will.

And, Jackson adds, don't point fingers, no matter how long the industries have neglected their responsibilities or how polluted the sites have become.

"Collaboration is what has worked for us," Jackson said. "In an urban area, there's just no putting the cow back in the barn."