On board the R/V Potawaugh, scientists were lowering cameras to scan the bottom of Harris Creek, trying to discern the quality of oyster habitat on the bottom. They were having little success.

Murky water obscured the images being transmitted. Finally, Jay Lazar began using a small, metal tong, roughly the size of a coffee can, to grab samples from the bottom.

Some grabs were mostly mud, others a mix of mud and shell. Then, he struck a patch of recently planted clam shell.

"Whoa! Look at that!" exclaimed Lazar, a scientist with the National Oceanic and Atmospheric Administration's Chesapeake Bay Office. Attached to the clam shells were a couple of tiny clear globs — oyster spat. The crew snapped photos with their cell phones, which within hours would stir excitement among others working on Harris Creek.

"By getting clam shells down there ahead of the spat set, we've created habitat that otherwise wouldn't have been available to the oysters," Lazar said.

It's the type of result scientists hope to see a lot more of in the coming years.

Harris Creek, a tributary of Maryland's Choptank River, is the site of the largest ever oyster restoration effort in the Chesapeake — or, for that matter, anywhere along the East Coast.

Over the next three to five years, state and federal agencies expect to spend up to $31 million converting hundreds of acres of river bottom into vibrant oyster bars by spreading shell, rebuilding reefs and planting hatchery-reared spat.

Over time, they hope a thriving, oyster community will transform the Harris Creek ecosystem with tens of millions of oysters that will help clear its murky water, creating conditions in which underwater grass beds can thrive and attract fish that like oyster reef habitats, such as spadefish, tautog, sheepshead and black sea bass.

"We are putting all of our eggs in the Harris Creek basket right now, with the notion that we hope to reach a tipping point in that system and create enough of a change that it is self-

sustaining," said Mike Naylor, who heads the Maryland Department of Natural Resources shellfish program.

Oyster bars were once a dominant feature of the Bay and its tidal tributaries, covering around 450,000 acres in the late 1800s. But overharvesting, disease and poor water quality caused oyster populations to plummet to 1 percent or less of their historic levels. Gone, too, is most of their habitat. Historic reefs were dredged away by harvesters, buried by sediment, or their shells simply dissolved over time.

Today's small, often isolated, oyster populations are frequently unable to produce enough offspring — or offspring that live long enough — to build new reef habitats at the rate that existing ones are being lost. In addition, their numbers are often too small to filter enough water to keep their own reefs from being silted over. The result is a continuing loss of habitat that gives larvae a shrinking amount of hard substrate on which to settle as they transform into tiny oyster "spat." In Maryland alone, the amount of suitable oyster bar habitat has declined 80 percent in the last 25 years, according to the DNR.

Oyster restoration projects over the last two decades have done little to change that overall trend. Past projects were often only a few acres in size. While many showed initial signs of success, they often succumbed over time because of increased disease, sedimentation, poor water quality, legal harvest, poaching — or a combination of those factors. Also, those small reefs simply did not provide a large enough area upon which oyster larvae could settle; many larvae were just swept away into areas with muddy bottoms.

The new "go big" strategy seeks to rehabilitate reefs in an entire tributary with the hope of reaching the tipping point where oyster populations are not only self-sustaining, but also expanding reef habitats and influencing local water and habitat quality. A federal Bay restoration strategy adopted in 2010 called for restoring self-sustaining populations in 20 Bay tributaries. Harris Creek is first on the list. Others include the Little Choptank in Maryland and the Lafayette in Virginia.

"We want to focus our resources on a few areas and see if we can really turn the tide in those areas," said Stephanie Westby, who heads NOAA's Chesapeake oyster restoration program. "And there is reason to believe that we might see some success."

Indeed, there is some evidence that larger efforts in portions of the Lynnhaven and Great Wicomico rivers in Virginia are showing signs of success.

But even those projects are dwarfed by what's on the drawing board for Harris Creek which, as one enters the Choptank River from the Bay, is the first tributary on the north. Over the next several years, agencies plan to improve or rebuild about 360 acres of reefs — or more than half of the bottom that is considered to be restorable. That's more than three times larger than anything that's been attempted in the Bay. Typical projects cover only a few acres.

The size stems from a recent consensus report developed by scientists and agency officials that suggests restoration projects likely need to cover 50–100 percent of the restorable oyster historic reef habitat in an area to become self-sustaining. In Harris Creek, that would translate into 300 to 600 acres.

"It is a huge improvement over the scattershot approach that we had before," said Bill Goldsborough, a fisheries scientist with the Chesapeake Bay Foundation. "We have evolved to this point where we recognize that we need to be attempting to restore whole systems, not just individual reefs. And that is going to be essential for the sustainability of restoration work in the future."

Many past restoration projects took place in areas poorly suited to oyster reefs so they would not compete with bars open to oyster harvesting. In other cases, restoration sites were eventually reopened to harvest. And many were so small it was difficult to catch poachers. The new effort aims to jump-start oysters where habitat conditions, relatively speaking, are still good. Harris Creek contains several of the best oyster bars in the state, according to a recent survey. In September 2011, the entire tributary was set aside as an oyster sanctuary where no harvests will take place.

Other factors that led state and federal officials to settle on Harris Creek are its relatively good water quality, so oysters can avoid stress from low-dissolved oxygen levels during the summer. The creek's circulation also helps to retain much of the oyster larvae it produces, rather than flushing them into the Choptank, which scientists hope will boost natural production. The creek's salinity level is low enough to reduce mortality from oyster diseases — which thrive at high salinities — but still high enough to allow decent spat sets.

Finally, Harris Creek is a size that officials believe is manageable. It is large enough that it might trigger an ecological change throughout the tributary, but a lot less daunting than trying to restore oyster populations in the entire Choptank or Potomac rivers.

"We are trying to achieve something that is much bigger than what we have done, but also have it be feasible," said Angela Sowers, of the Army Corps of Engineers Baltimore District. "I think we need to show success at this level, and show that it can be done, before we tackle those really large ones."

Actual restoration sites in the river were pinpointed with side-scan sonar to identify areas where solid substrate remained, and to avoid areas that were simply mud. The sonar findings were verified with follow-up inspections because sometimes bottom areas that appear solid to sonar may actually be buried by a layer of sediment, making them unsuitable for oyster sets.

Scientists also surveyed to determine where oysters remained, and how many there were. Any areas with thriving populations, after all, would not need restoration.

The results show just how daunting the task will be. The restoration target is to have at least 15, and preferably at least 50, oysters per meter, which is the restoration goal. Only three acres met that criteria, and those were areas were restoration efforts had taken place in the past, according to surveys conducted in the river.

Based on that survey work, 157 acres that have adequate substrate will be "seeded" with hatchery-produced spat. Roughly 217 additional acres need reef construction because, while they supported reefs historically, the bottom is no longer suitable for oysters.

This year, the agencies, addressed about 10 percent of the bottom that needs solid substrate, covering 22 acres with either granite or clam shells. Working with the nonprofit Oyster Recovery Partnership, they seeded another 88 acres with spat attached to oyster shell that had been reared in a hatchery at the University of Maryland Center for Environmental Science's Horn Point Laboratory.

The good news, according to Kennedy Paynter, a scientist with the University of Maryland Marine-Estuarine- Environmental Sciences Program, is that bottom surveys conducted in Harris Creek and the nearby Little Choptank showed that areas in both tributaries that had the best substrate also had the greatest number of oysters. And some of the highest numbers were found on bars that had been the target of recent restoration efforts. Of the estimated 6.5 million oysters in Harris Creek, 30 percent were on 20 acres that had gotten some type of restoration work in the past.

"At least for the last few years, the methods we have been using to do restoration have been working," Paynter said. "We can refine them and get better at it."

The bad news, according to Paynter: "We realized there isn't as much good acreage as we thought." But the new restoration approach, he said, offers a chance to change that. "Over the past 15 years, we have spread restoration efforts through the counties to be politically correct," Paynter said. Even if the projects were successful, they were typically too small to influence local ecosystems, increase spat sets or increase fish populations. The new large-scale approach, he said, "is pretty exciting."

But scaling up from projects that are a few acres to ones the size of Harris Creek creates obstacles, and Harris Creek is helping officials figure out how to deal with issues they will face with future tributary-scale efforts.

One obstacle is being able to access enough restoration sites to cover at least 50 percent of the potential oyster acreage. A lot has changed since the days when 450,000 acres of reef were found in the Bay, and much of what was once oyster habitat is now used for other purposes.

In Harris Creek, restoring 300–600 acres means that work needs to take place on historic habitats in less than 8 feet of water. Getting the needed permits for that work from state and federal agencies, which are concerned about impacts to navigation, has been a challenge. "Our society right now is not used to having large-scale, broad oyster reefs," Sowers said. "So we have become accustomed to navigation without them."

Poaching has been a severe problem at other restoration sites. The DNR, by making all of Harris Creek a sanctuary, will make poaching more difficult, and is planning beefed-up "24/7" policing that takes advantage of new technologies, according to the DNR's Naylor.

The biggest obstacle by far, though, is finding enough substrate to rebuild reefs. Most agree that oyster shell is the best material, but it's in short supply. Ironically, efforts to promote aquaculture to reduce harvest pressure on wild oysters has contributed to the problem. Oyster growers often outbid the state for oyster shell. "They are essentially buying the shell out from under us," Naylor said. "Shell has gone from being a waste product to a commodity in just a few years."

The state is exploring the possibility of importing shell from a quarry in Virginia that produces cat litter, where a layer of mixed fossil shells was recently uncovered.

This year and next, much of the substrate is being created by using clam shells from the ocean, and granite. That's upset watermen already angered by having what they considered a productive oyster river placed off-limits to harvesting.

Russell Dize, who lives on Harris Creek and has worked the Bay's water since 1959, said watermen widely opposed the decision to use granite — which isn't naturally found on the bottom of the creek — for the project.

Establishment of the sanctuary already eliminated oyster harvests, he said, and the granite on the bottom has made crabbing more difficult as well. "There is something about the granite that makes the crabs behave differently," he said. "If it's just shells, it's not so bad."

Whether the Harris Creek project succeeds is not totally in the hands of agencies or scientists. Despite the huge effort, some of the factors that can contribute to failure rest with Mother Nature. For instance, a prolonged period of drought can dramatically increase the prevalence of lethal diseases. Naylor is already concerned that dry conditions this summer could lead to an increase in disease which could, in turn, lead to increased mortality next summer.

That would drive up restoration costs if large areas need reseeding to replenish oyster numbers.

Mother Nature could also lend a helping hand if she provides conditions favorable to larval production that result in large spat sets on newly created reefs.

"If we get good spat sets, that can really reduce costs a lot," Westby said.

And that is why those working on Harris Creek were excited Lazar's spat photos. They were found in an area that had not been seeded with hatchery spat. Instead, they were the result of natural reproduction that had taken advantage of the newly created substrate.

For the project to be considered a success, a lot more of that will need to be seen in coming years and decades.