When Rick Unger was a boy, he and his father would fish from the breakwall where the Cuyahoga River enters Lake Erie.

“I remember the smell,” says Mr. Unger, now 59. “I remember the oil slicks. I remember the fishing not being very good.”

The Cuyahoga was then so polluted that the surface occasionally caught fire. Erie was considered a “dead” lake; in summer floating mats of stinking blue-green algae consumed so much oxygen in the water that large areas of the lake were rendered lifeless.

But in 1972 Congress passed the Clean Water Act, one of the most far-reaching and ambitious environmental laws ever enacted in the United States. The act cut industrial pollution, set new goals for the health of the nation’s waters, and provided billions of dollars to help cities build and upgrade sewage treatment plants.

The effect on the Cuyahoga and Lake Erie was swift and dramatic. Within years, the algae blooms disappeared. The Cuyahoga stopped burning. Fishing improved.

“We had a terrific lake again,” says Unger, now a charter boat captain and president of the Lake Erie Charter Boat Association. Lake Erie became known as the “Walleye Capital of the World.”

Now, 40 years later, Lake Erie is once more in trouble. In recent summers large blooms of toxic algae have returned. In 2011, the worst year so far, there were days when the algae was so thick that Unger couldn’t take his customers fishing. He once drove his 27-foot Sportcraft boat 14 miles straight north from Cleveland before he gave up and turned back. “I never got out of the algae,” he says.

The recovery and decline of the Lake Erie ecosystem offer a vivid illustration of both the successes and failures of the Clean Water Act in cleaning up and protecting the nation’s waters.

Experts on environmental history and policy say that, since the act, much progress has been made: cleaning up rivers and lakes, protecting estuaries and wetlands, and curbing pollution from industry and municipal sewage – problems that were acute by the 1970s despite earlier efforts to stop pollution.

The Environmental Protection Agency (EPA) estimates that in 1972 two-thirds of the waters in America were unfit for fishing or swimming. Today, it says, that amount has been cut in half, to one-third.

At the same time, shortcomings in the Clean Water Act and its implementation have left the nation with problems that are being addressed too slowly or hardly at all, experts and environmental advocates say. Here's a synopsis of some of these problems.

• Runoff from urban areas carries pollutants from streets and lawns into lakes and rivers. During storms, this runoff can overwhelm sewer systems, sending untreated sewage into nearby waters. Many cities are working to separate sewers that carry rainwater from those that carry sewage. Some, like Philadelphia, Milwaukee, and Washington, D.C., are also promoting the use of “green infrastructure” to reduce runoff.

• Pollution standards for different industries – standards that determine what the industries can put into the water and what they can’t – are out of date. Plus, new pollutants are emerging, including pharmaceuticals and cosmetics.

“People are inventing new chemicals faster than we can figure out what to do about them,” says William Hines, a professor of law at the University of Iowa in Iowa City.

• Aging infrastructure – including treatment plants and sewage systems that in some cities date to the 19th century – is a growing threat to water quality. Even sewage treatment plants built with federal money in the early years of the Clean Water Act are in need of upgrades.

“If we don’t reinvest in that infrastructure, we’ll start falling backwards again, in part due to population growth,” says Robert Adler, a professor of law at the University of Utah in Salt Lake City and the author of a book on the Clean Water Act.

• The act left largely untouched the leading cause of pollution today, known as “nonpoint” pollution. The largest source of this is runoff from agriculture. Each year, for example, fertilizer from Midwestern cornfields washes down the Mississippi River and creates a “dead zone” in the Gulf of Mexico. Farm runoff is an ongoing problem in many smaller bodies of water, including Chesapeake Bay, Lake Erie, and many other lakes and rivers around the country. Under the Clean Water Act, states have been identifying thousands of bodies of water polluted by excess nutrients from agriculture. But the act gives the federal government little power to regulate agricultural pollution. “We keep talking about plans, but there’s very little execution,” says Mr. Hines.

The Clean Water Act was one of a trio of sweeping environmental laws enacted in the early 1970s, including the Clean Air Act (1970) and the National Environmental Policy Act (1970). It came at a time of growing interest in the environment and of readiness to extend the powers of the federal government.

Environmental regulation in the United States dates to the 19th century. But the Clean Water Act was different in that it greatly expanded federal powers to curb pollution, a job previously left to the states. By allowing private citizens to bring lawsuits over pollution, the Clean Water Act also opened up new opportunities for citizen action.

For example, Heal the Bay, an environmental group in Los Angeles, got started when a group of citizens invoked the Clean Water Act in a fight to clean up Santa Monica Bay. “We’ve been working the Clean Water Act ever since,” says Kirsten James, the organization’s water quality director.

In part, the Clean Water Act was a victim of its own overarching ambitions. It set standards that turned out to be impossible for the country to meet. The act said that by 1983, all waters should be clean enough for fishing and recreation. By 1985, it said, the discharge of all pollution should be stopped.

“It struck me at the time that it just wasn’t realistic,” says Hines, a critic of the act when it was enacted. Today, he says, “I feel kind of sad that we’re not further down the road.”

After four decades, much remains to be done. According to a recent EPA survey, 54 percent of the nation’s river miles, 69 percent of its lakes and reservoirs, 66 percent of its estuaries, and 85 percent of its wetlands are in some way impaired.

Of course the Clean Water Act didn’t just set goals; it came with large sums of money to reach them. From 1970 to 1995, the federal government spent $61 billion to help cities upgrade and build sewage treatment plants. This sharply reduced the amount of organic pollutants, especially nitrogen and phosphates, that were overloading the nation’s waters.

But federal largess has dwindled. By 1987, the assistance had shifted to a $16 billion revolving loan fund. Mr. Adler says as much as a trillion dollars may be needed over the next 20 years. “The remaining capital needs … are staggering,” he says.

Lake Erie was one of the leading beneficiaries of the Clean Water Act. Its restoration was the “best example of ecosystem recovery in the world,” says Jeffrey Reutter, a biologist at Ohio State University. The main reason was that improved sewage treatment around the lake reduced the amount of phosphorus, an important nutrient for algae, getting into the water.

Since the mid-1990s, however, the amount of phosphorus has begun to rise again. Some still comes from municipal sewage plants, but the chief culprit is farming.

Steve Davis, a watershed specialist for the Natural Resources Conservation Service in Lima, Ohio, says farmers have in many ways improved their practices. Many no longer plow their land but use “no till” methods. At the same time, they have taken to applying fertilizer in the winter, when it is more likely to wash off the fields.

Mr. Davis encourages farmers to adopt conservation methods such as using cover crops in winter, planting buffer strips along creeks and other waterways, testing soils to determine how much fertilizer their fields really need – and refraining from applying fertilizer in winter. Federal grants offer incentives.

“It’s a big challenge and a complicated problem, but a lot of people are working on it,” he says.

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Unger and his fellow charter captains do their part by taking farmers out on Lake Erie to show them what farming is doing to the lake.

One farmer gazed upon the pea-green water and told him, “I don’t know whether to kiss you or hate you. I’m not going to be able to apply fertilizer without thinking of what you stand to lose.”