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The Chesapeake Bay is where we go next. It's America's largest estuary, and it has undergone decades of clean up efforts at a cost of billions of dollars. Yet it remains heavily polluted. So, today, the Environmental Protection Agency is scheduled to announce a new draft of a plan, as it tries yet again to save the bay. Scientists are still working on this plan.

NPR's Christopher Joyce recently hopped aboard the research ship Rachel Carson to see what progress they're making.

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CHRISTOPHER JOYCE: Dave Nemazie steers a 15-foot skiff through the choppy waters of the Wye River, one of the bay's numerous tributaries. Upon shore, soybean and corn fields give way to housing developments. Nemazie is with the University of Maryland's Center for Environmental Science. He says 30 years ago, people knew the bay was sick.

Mr. DAVE NEMAZIE (University of Maryland's Center for Environmental Science): But I think there was also really a sense that, you know, in a few years, some hard work, we'll get over this. And we've learned both in practice, but also just living on the bay, that that's certainly not the case.

JOYCE: Some things are better: striped bass are back in big numbers. Several rivers, like the Potomac, are cleaner. But there are more dead zones, where almost nothing lives. Sea grasses are struggling and once-great harvests of oysters and crabs are a memory.

The EPA has now vowed to start over, to do better, but scientists first have to figure out what's actually happening in and especially under the water. That's what determines the bay's basic chemistry.

Mr. WALTER BOYNTON (Marine Scientist, University of Maryland's Center for Environmental Science): We've been basically making a map of what the sediments are doing to the water in Chesapeake Bay.

JOYCE: That's Walter Boynton, a marine scientist also with the science center. He's aboard the Rachel Carson taking sediment cores. The crew lowers a metal canister into the murky water, where it sinks to the bottom and grabs a mud sample. Then it's hauled back on board and its contents retrieved.

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Unidentified Female: There it goes.

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JOYCE: These piles glop are like biopsies. They indicate where the bay is healthy and where it's dying. That will help determine where the EPA needs to crack down on pollutants. Boynton says dead sediments are easy to identify.

Mr. BOYNTON: They almost feel like - if you were making a pot of Jell-O and it hasn't quite congealed yet.

JOYCE: Dead sediments are basically mud with little or no oxygen. Clams and worms and microscopic plants at the bottom of the food chain down in the mud need that oxygen. But the bay is oxygen-starved. What it's got instead are nitrogen and phosphorous - way too much of it.

The extra nitrogen and phosphorous come mostly from sewage, cars and fertilizer. They act as nutrients for algae, which gorge on them and grow into huge, floating blooms. When the algae die and decompose, that sucks oxygen out of the water. And that's deadly.

Mr. BOYNTON: The key issue in the bay program is reduce the amount of nitrogen and phosphorous and dirt getting into the bay. We, frankly, need to know: Where does this stuff come from? How long does it hang out here, and where the heck does it go?

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JOYCE: Biologist Kristin Politano taps a canister of sediment to get oxygen bubbles to rise. She learned about nutrient pollution in Florida, but in some ways, it's just the same here. Scientists can map the pollution hot spots, but someone has to follow them back to source to fix the problem.

Ms. KRISTIN POLITANO (Biologist): I mean, people get upset about what's going on in the bay. What they have to realize is that a lot of these problems are coming from the upper watersheds themselves. You have to look at restoring headwater streams and rivers and things like that before you are going to see an improvement in the water quality that's coming into the bay.

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JOYCE: Once Boynton measures the oxygen and nutrients in these sediments, the information goes into computer models that EPA can use to figure out where, within this 180-mile-long bay, it needs to spend its new cleanup money, and where to crack down on polluters.

Like most scientists who've studied the bay, Boynton says progress has been frustratingly slow. But he's optimistic about this new start.

Mr. BOYNTON: I still maintain that if we start seeing big, big changes in nutrient loads, we will see positive changes in the bay very quickly. And by very quickly, I mean a year or two.

JOYCE: Making that happen, he adds, is up to politicians and the people who vote for them.

Christopher Joyce, NPR News.

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INSKEEP: And you can take a virtual voyage with a team of Chesapeake Bay researchers and see just how messy their job can be at npr.org.

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INSKEEP: You're listening to MORNING EDITION from NPR News.

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