With a whirring noise, a powerful winch began hauling 160 feet of line, weighed down by six fish traps, aboard the Bay Commitment.

The first trap pulled from the soft bottom of this part of the Little Choptank produced an oyster toadfish and a white perch.

“It is surprising to find an oyster toadfish here,” remarked David Bruce, an ecologist with the National Oceanic and Atmospheric Administration’s Chesapeake Bay Office.

Oyster toadfish, after all, are a species more associated with oyster bars than with mud and sand bottoms.

And, they’re noted for something else.

“Oyster toadfish have a mean bite,” cautioned Madison Fort, an intern with the office.

Bruce nodded. He’s been bitten before. The squirming fish were gingerly removed from the wire trap, measured and tossed, live, back to the river.

The winch pulled up the next trap, which had an eel, and then the third, which had a blue crab.

The fish survey being undertaken by the five-person crew of the Bay Commitment — a NOAA research vessel — is one of several studies under way to quantify the ecosystem benefits derived from restored oyster reefs.

Off in the distance, a barge with a large crane was placing granite into the water — the foundation for some of the roughly 400 acres of oyster restoration that the Maryland Department of Natural Resources is planning for this Eastern Shore river.

Oysters were once considered a keystone species in the Chesapeake Bay, whose reefs provided habitat for a diverse community of fish, shellfish and other types of aquatic life. But disease, overharvesting, loss of habitat and pollution have driven populations down to less than 1 percent of their historic level.

To reverse that trend, state and federal officials in recent years have moved forward on a new large-scale oyster restoration strategy. Unlike small projects of the past, which generally covered only a few acres, the new projects would blanket select areas of tributaries with hundreds of acres of constructed reefs.

The Little Choptank is the second large-scale project in Maryland. The first, a 377-acre project in Harris Creek, located on the north side of the Choptank River, is nearing completion. Work is expected to start in the Tred Avon, also a Choptank tributary, this winter. In Virginia, work has been done in both the Great Wicomico, and Lynnhaven, and is in the planning stages for the Piankatank and Lafayette.

The Chesapeake Bay Watershed Agreement signed earlier this year calls for such projects to restore oyster populations in 10 tributaries by 2025.

But the projects have huge price tags. The Little Choptank could cost $25 million; the Tred Avon more than $14 million; and Harris Creek nearly $30 million.

The intent is that the large-scale reefs would not only become self-sustaining, but become dominant ecological features in those tributaries by boosting fish and shellfish production and improving water quality.

But most of those benefits are assumed. No one can actually say what the public is buying when it spends tens of millions of dollars on an oyster restoration project, other than the rock put down to create a solid substrate, oyster shells to cover the rock and millions of hatchery-reared oyster larvae planted on the shell with the hope that they’ll thrive.

To start answering part of that question, the biologists on the boat were collecting information about the fish community on various substrates in the river before restoration takes place. They began collecting their data last year, and will continue in order to see how — and whether — huge new oyster reefs affect fish abundance in the Little Choptank.

“The main goal is to try to detect a difference before and after oyster reef construction,” Bruce said.

Most past oyster projects were primarily aimed at replenishing areas so oysters could be harvested. The value of those projects could be measured from the amount of oysters harvested.

Today’s large-scale projects, like the Little Choptank, take place in sanctuaries where harvesting is prohibited. Estimating their benefits means understanding — and potentially being able to put a dollar value on — the services they provide: whether they actually produce more fish, cleaner water, healthier aquatic communities and enhanced recreational fishing opportunities.

While sanctuary-based projects have taken place in the past, they typically covered only a few acres, usually in large tributaries. Identifying changes attributable to such small projects was almost impossible. But the new projects often cover hundreds of acres in relatively small tributaries. Their goal, in fact, is to cover enough area to trigger systemwide changes throughout the tributary.

“All the prior restorations we have done have been fairly small-scale, just a few acres, whereas we are talking hundreds of acres here,” said Howard Townsend, an ecological modeler with the NOAA Bay Office. “How that ends up changing the fish communities is something we wouldn’t have a good handle on if we just looked at an existing site where small-scale restoration has been implemented.”

In addition to the survey being done by the biologists on board the Bay Commitment, NOAA is funding related research at the University of Maryland and the Virginia Institute of Marine Science.

Some studies are looking at whether restored reefs in certain areas have the potential to remove large amounts of nitrogen from the water, transforming it to a harmless gas through denitrification.

Others are looking at the benthic communities — reefs once supported a rich abundance of worms, small clams and other invertebrates that helped fuel the Bay’s food web. Scientists want to see whether, and how quickly, such communities would return and to estimate to what degree they might increase fish populations over time.

Not all of the benefits necessarily accrue locally. Black seabass are primarily harvested in the ocean, but their young live in estuaries and like oyster reefs. One of the things biologists would like to know is whether more oyster reefs in the Bay might mean more adult black seabass in the ocean.

Eventually, scientists hope to be able to model not only what oyster restoration means for oysters, but also for fish populations in the local tributary and elsewhere, and what that is worth to the economy. They even hope to be able to estimate the value of any pollution benefits, such as nitrogen removal, attributed to a restored reef.

“Ultimately, this is going to validate an oyster reef ecosystem services model,” Bruce said.

But developing the model, and estimating benefits, requires lots of field work.

The Bay Commitment has been visiting sites in the Tred Avon and Little Choptank each month.

Each site requires two days of sampling, which is conducted once a month from May through October.

On the first day, the crew places eight sets of trap lines on non-shell substrate, usually mud or sand, and another eight on shell bottom. Each line contains six traps of different types, mostly baited with razor clams or menhaden.

On the second, they reel in the wire traps and measure everything that’s been caught. By the end of the second day, the boat is stacked high with all manner of traps: eel pots, finfish traps; minnow traps; crab traps; spot pots; and black sea bass pots.

“Every pot is designed to catch different size fish,” said Andrew Turner, a fisheries biologist with the NOAA Bay Office. “These try to represent all types of species that might be around this time of year.”

So far, the pre-restoration sites don’t show a lot of species. Most have yielded only about 10 species of fish — “not a lot of diversity,” Bruce noted. The greatest diversity comes in midsummer, with the catch dropping sharply in the fall. Last November’s catch, Bruce said, was zero.

Fortunately, the scientists were fishing for data, not a living. And the real payoff will come years down the road — if the numbers start to show that thriving oyster reefs transformed some of the Little Choptank’s muddy bottom into a thriving fish factory like those that may have existed centuries ago, before anyone needed to measure their benefits.