“Well I love that dirty water. Oh, Boston, you’re my home.”
— “Dirty Water” by Ed Cobb

The last vestiges of winter are hanging around on a late March day in Boston. But with a light wind and temperatures just above freezing, it’s pleasant enough for the Charles River to resume its role as the city’s gym. Students crew their boats along a placid stretch between the Harvard and Boston University bridges. Young women bundled in down vests jog along the Esplanade toward Back Bay. Just below the Longfellow Bridge, sailboats bob in the water. Not even the looming threat of a snowstorm can derail this feeling of springtime.

It’s been a long and pleasant spring indeed for the Charles, a river once so dirty that it inspired native son Ed Cobb to compose the song, “Dirty Water,” which became a hit for The Standells in 1966. Back then, raw sewage floated in the Charles. The river was so full of toxins that blooms of pink and orange floated to the oil-slicked surface. Harper’s Magazine writer Bernard DeVoto called it “foul and noisome…unlikely to be mistaken for water.”

Like many other urban U.S. waterways, the Charles saw a flow of activism in the late 1960s and early 1970s, when the U.S. Congress passed the Clean Water Act. But Boston’s momentum for clean water never wavered. In 2007, the river earned a “B plus plus” on its annual report card; that same year, it launched its first Master Swim Race, now an annual summer tradition. In 2011, it earned the prestigious international Riverprize.

How did Boston do it? What can Chesapeake Bay cities learn from its successes?

Robert Zimmerman, longtime director of the Charles River Watershed Association, founded in 1965 to address the river’s problems, spoke at a 2010 conference organized by the Waterfront Partnership of Baltimore to announce its Healthy Harbor Initiative. (That plan calls for Baltimore’s Inner Harbor, still a dangerous cocktail of nitrogen, phosphorus, bacteria and toxins, to be swimmable and fishable by 2020.)

For those who think the goal is impossible, Zimmerman’s message is this: It isn’t easy, but it is possible. Here’s how Boston did it:

Start with a strong and smart organization nimble enough to act.

The Charles River Watershed Association’s building is not in posh downtown Cambridge; it’s in suburban Weston, still along the river, but in a much less-expensive locale. Inside, office furniture is dated, files are piled high, and the toilet has a warning that its septic system is delicate.

None of that harms morale. Most of the organization’s 10 employees have been around for a decade. A knowledgeable staff makes a difference, Zimmerman said. So do in-house scientists, planners and attorneys.

“When we say something, the powers that be tend to listen. We’re a credible threat, and they know it.”

Do your own science.

When Zimmerman came to the Charles River Watershed Association in 1993, he assumed one of Boston’s many great universities would conduct water testing on the river. He quickly learned that the universities had other priorities. People needed to know if it was safe to be on the water that day, or that week. So the organization developed its own lab and conducted its own tests. It worked with the EPA to verify the science so that the organization’s tests would have the same validity in court as if the EPA scientists had done the work themselves. In the summer, the organization monitors some parts of the river three times a week.

“You really need an independent organization that takes it upon itself to find out why things are the way they are,” Zimmerman said. “How does it get polluted? When does it get polluted? What’s the interaction with sediments? What happens during a rainstorm? Why are there fish kills for no apparent reason? Everybody offers an explanation, but that explanation may have no basis in ongoing fact. Besides, if you don’t do your own tests, how do you know when things are getting better?”

Tackle the point sources smartly.

Boston’s biggest problem in its early days was sewage. In 1983, the Conservation Law Foundation sued federal and state authorities to stop municipal sewage treatment plants from discharging their waste directly into Boston Harbor. By the early 1990s, the Massachusetts Water Resources Authority had taken over the wastewater treatment for the 43 communities that make up the metropolitan Boston area. In addition, the authority put in a plan to end combined sewage overflows.

The project solved a major problem in that it treated millions of gallons of sewage a day. But as the sewer pipes passed through streams and groundwater, fissures in the pipes brought in more water so that the system ended up treating water that belonged in rivers and streams. So, approximately 160 million gallons of groundwater that the city needs to stay in place is leaking into the treatment system, being treated, and being discharged into Massachusetts Bay. Not only is that hurting waterways, but it’s also leading to home collapses because the pilings under the buildings need to be submerged.

“It fixed the problems it was designed to fix,” said Kate Bowditch, director of projects. “But we’re dewatering East Massachusetts.”

Now, the Charles River Watershed Association is developing a “Smart Sewer” plan that returns treated water to the ground from where it was first pumped. Littleton, a river community northwest of Boston, was the first to study this approach. Two other towns, Wrentham and Sherborn, have been studying Smart Sewering in their towns.

Don’t shy away from big projects.

When developers wanted to turn the defunct Waltham Watch Factory into a top-notch mixed-use facility, they contacted the Charles River Watershed Association. Pallavi Mande, director of the organization’s Blue Cities project, helped the developers formulate a plan for rain gardens, native plants and attractive downspouts that divert the water. The result is a showplace with the river as a backyard. The lofts are one of the most desirable addresses in the area.

Maps educate people.

One of the watch factory’s highlights is a watershed map. It’s right near a shed where residents can keep their kayaks. Looking at the map, residents of Waltham can see how what they put into the river flows downstream to Cambridge and finally to the Boston Harbor.

Understand, respect and protect natural systems.

Much of the organization’s work focuses on returning the river to its natural flow. Floods in the 1950s and 1960s convinced officials that Boston needed a levee system, like the one New Orleans had. Instead, early leaders of the Charles River Watershed Association persuaded the U.S. Army Corps of Engineers to buy and protect 8,000 acres of wetlands along the river. That decision has saved Boston from devastating floods and provided important habitat.

Use lawsuits sparingly.

Though it was a lawsuit that forced the government’s hand on Boston’s sewage issues, Zimmerman said his group tries every means of dispute resolution before going to court. As a result, his staff attorney rarely files lawsuits.

There’s never money for improvements; they have to pay for themselves.

The organization is looking at waste-to-energy projects as part of its Smart Sewer plan.

Put it all together in a demonstration project.

Too often, Zimmerman said, organizations work in silos. They daylight one stream, or they repave a couple of alleys with porous surfaces. A better option is to take a small subwatershed, implement a mix of practices and harness the power of them working together, then monitor the project to see continued progress.

Voluntary actions are nice; regulatory hammers are better.

The organization helped established a total maximum daily load for its river, one of the nation’s first. It also helped to persuade the EPA to use a little-employed strategy of tackling stormwater — the Residual Designation Authority. This rule, which is part of the Clean Water Act, requires owners of sites larger than two acres to retrofit their stormwater technologies to capture 65 percent of the phosphorus. Several environmental advocates lobbied the EPA to use the RDA authority in the Chesapeake Bay, but the agency declined to do so.

Don’t assume you can’t do it.

The Charles River flows for 83 miles and drains a watershed of 308 square miles that is home to more than a million people. Its problems were daunting. But, Zimmerman said, he and his staff are not superheroes.

“Do you know how many times in the last 20 years that people (from other cities) have called, listened to what we say, and then told me, ‘well, that’s Boston, it can’t be done here?’ We get those calls about once a week,” Zimmerman said. “I never accepted the notion of doing what I was supposed to do. Once you understand how something got messed up, you can figure out how to fix it.”