Martin Suuberg balanced precariously on a muddy bank and stretched with a net to reach what looked like a soggy old tennis ball.

"You thought I was going to go in?" he said. "There was a couple of moments where I thought I might too."  

All the stuff we put on the ground -- the tennis balls, cigarette butts, styrofoam, it all ends up somewhere — like the Charles River. And hopefully a volunteer picks it up at the annual Earth Day cleanup — like Suuberg, who also happens to be commissioner of the Massachusetts Department Of Environmental Protection. There's also a group of 20-somethings who live near this bend in the river, in Watertown, that volunteer together every year.

"We found two needles pretty much off the bat," one volunteer says.

"America really does run on Dunkin'," says another. "It's proven in the trash."

"Broken glass from needles," says a third. "The needles were all capped, so we have a responsible group of junkies in this city."

For everything they pick up and put in a bag, there’s plenty more they can’t see in the river’s foamy grey eddies — oil, salt, fertilizer, pesticides. Altogether it’s called "nonpoint pollution," because it doesn’t come from one "point source," like a drainage pipe from a factory. It comes from all over — your neighbor’s lawn, the baseball field down the street, or the farm you pass on the highway.

All of that gets swept up when it rains a lot, and water can’t seep slowly into the ground. Everything that was on the ground suddenly becomes mobile — flowing toward the closest lake, river or ocean.

"That may be a technical point, but it’s critically important," Christopher Kilian, an environmental lawyer with the Boston-based Conservation Law Foundation. "Because under the Clean Water Act, if something’s a point source, it’s regulated and subject to enforcement. Something’s a nonpoint source, it is not."

We know the Clean Water Act worked. University of Iowa environmental engineer Jerald Schnoor says industries stopped pouring pollution into waterways unchecked.

"Under the Clean Water Act we have cleaned up our waters since 1972, quite a lot," Schnoor said. "Industry and municipality both, we have investing in more than $100 billion in cleaning up the nation's water. But now those water quality has roughly plateaued."

Our water has stopped getting cleaner. But it’s still saturated with huge amounts of nitrogen and phosphorus that feed thick algae blooms. They blanket water surfaces with green goo that smothers everything underneath.

"Last summer, the city of Toledo, they could use water from Lake Erie," Schnoor said. "There were a few days when we couldn't use it because of algae bloom."

Scientists are coming to a consensus. Schnoor says they think nonpoint pollution is having a profound effect on our rivers, lakes and oceans. The impact gets worse with intense rainstorms that scour more stuff off the ground. That’s exactly what scientists say New England will see as climate change advances.

Forrest Kennedy runs one of the labs at the University of Massachusetts Dartmouth School of Marine Sciences in New Bedford, one of the largest scallop producing ports in the country, where they’re studying some of the impacts of nonpoint pollution.

Kennedy lifts a live scallop from the water. "This is actually brought in by the scallopers," he said. 

It looks like a big oyster.

Nonpoint pollution threatens scallops because as it breaks down, it makes the ocean water around it more acidic. And shellfish have trouble building their calcified shells in water that’s too acidic.

Scientists always expected ocean water to get more acidic, but not because of nonpoint pollution. They thought carbon was the only real culprit. Oceanographer Cindy Pilskaln says seawater soaks up about a third of the carbon, or C02, we put in the environment. Without the oceans, the climate would be changing a lot faster.

“We just didn’t worry about it because — we as a community — because this large volume of water was going to take up a lot of C02," Pilskaln said. "We didn’t really think that it’d come to a point where we’d actually start to see, through long-term monitoring, pH changes and organisms having a hard time making calcified shells. Which is what we're now seeing."

It’s now clear that increased flooding caused by climate change is making nonpoint source pollution worse, accelerating the acidification of oceans and threatening a $400 million shellfish industry. But so far the increase in acidity has been small.

"Although it’s much larger than people though it would be," said Brian Rothschild, a fisherman and scientist who co-founded the UMass Marine Sciences school. He said fisherman worry about more immediate problems than acidification.

"Most fishermen are concentrating on day-to-day regulatory issues and they really don’t think about the environment or scientific change." Rothschild said. "Mr. or Ms. fisherman is really more concerned with that than changes with acidity, which seem abstract and remote but are very important."

To deal with the small increase in acidity, some shellfish farmers are dumping, essentially, antacids into breeding grounds. The fishing industry is funding research to learn more. Some states have set up ocean acidification task forces; the Massachusetts Legislature is considering doing the same.

And this is one of the rare issues where individuals who want to can really have an impact. It’s easy. Stop putting stuff on the ground.

This story was reported with assistance from Annie Phuong Nguyen. To explore the simple yet vast subject of water, WGBH News has partnered with the American Academy of Arts and Sciences — this is the second of five installments.