Two divers who explored the submerged floor of inner Quartermaster Harbor last week were pleased with what they found — flat, featureless muck. Or as ecologist Brian Allen put it, “A whole lot of nothing.”

It wasn’t a surprise: Inner Quartermaster has layers and layers of silt and few fish, due to its notoriously low levels of dissolved oxygen.

But what that flat, muddy sea floor will provide is a good spot to sink an anchor for several months, which in turn will open the door to an innovative experiment in how to heal a place like Quartermaster — an estuary suffering from a massive overload of nutrients.

The two divers — both employed by the nonprofit Puget Sound Restoration Fund — are part of an effort to see if native mussels can be recruited to help restore Vashon’s ailing inland sea.

The mussels will cling to ropes hanging from the bottom of a specially designed raft anchored to the sea floor, Allen explained, where they’ll do what mussels always do — take in nutrients and convert them into protein, filtering out particulates and cleaning the water in the process.

But they won’t just float there: The mussels will be contained within a cylinder, with in-take and out-take valves. That will enable researchers to assess the water quality as it goes in and goes out — which means researchers will be able to measure with a fairly high degree of certainty how great a role mussels can play in taking up Quartermaster’s excess nutrients.

Mussel cultivation as a way to clean up polluted bays and estuaries is happening in other parts of the world — from the fjords of Sweden to the South China Sea. But it has yet to be attempted in Puget Sound, where concern about its health has been mounting over the past several years.

Betsy Peabody, who heads the Bainbridge Island-based Puget Sound Restoration Fund, said the pilot project will underscore a message she has been preaching for years: “The marine system can be an ally.”

It doesn’t get Islanders off the hook, she added. The sources of those nutrients — nitrogen and phosphorous from failing septic systems, lawn fertilizer and other human activities — still need to be addressed, she said.

But communities, when attempting to clean up a bay, often look to what she called “engineered solutions,” such as large wastewater treatment plants. That won’t work on a place like Vashon, where the costs would be too high and the footprint too great, she said.

What’s more, she said, the pilot project will involve Islanders — including high school students and other volunteers her organization plans to recruit to collect the native mussels, help build the raft, even take water measurements. And that, too, she said, will have a beneficial impact.

“By doing something cool and interesting in inner Quartermaster Harbor, we start to build a group of people really interested in that system, how it functions, the role of shellfish and how they can be used as an ally,” she said. “It’s still about source control. This is not meant as a way to distract us from the larger purpose. It’s about galvanizing support for that larger purpose.”

The project comes at a time of heightened focus on Quartermaster, a bay many ecologists and scientists think is in bad shape because of its nutrient-overload and the low oxygen levels that result from all those excess nutrients. King County officials recently declared a long swath of shoreline along outer Quartermaster a marine recovery zone and have begun talking to homeowners about repairing or replacing failing septic systems. County and state researchers, armed with a federal grant, are also attempting to map the sources of the bay’s excess nutrients: Livestock could be part of the problem, or even alders, which fix nitrogen from the air and put it into the soil.

The county is helping to fund Peabody’s research. She recently received a $50,000 Waterworks Grant for the pilot project. Ken Pritchard, an Islander who manages those grants for the county’s Department of Natural Resources and Parks, said the project will likely answer a lot of fundamental questions about how an approach used in other parts of the world will play out in Puget Sound.

“She has the right people looking at this,” he said.

At the same time, county officials don’t think mussel cultivation will become the “silver bullet” that will clean up Puget Sound, he said.

“You’ve got to work on many fronts. The mussel raft is simply another tool that is untried and that may be useful,” he said. “It’s one more thing that could help do the trick.”

The project has promise in yet another way, Pritchard and Peabody said. At some point, project managers will harvest the hundreds of plump mussels beneath the raft and grind them up for either chicken feed or compost, creating what ecologists call a closed-loop system.

After harvesting them, researchers will conduct tests on the mussels to find out whether metals or other pollutants reside in their tissue, Peabody said. If not, they could be deemed organic; if so, they’d search for other applications, she said.

In Sweden, several experiments are underway trying to determine the best use of mussels, including use as chicken feed, which is gaining some traction, said Jan Cassin, an ecologist with Parametrix, a consulting firm in Bellevue, and someone who is studying the issue in Sweden. “It’s cheap, high-quality chicken feed,” she said.

At some point, if this approach were to prove effective, mussel rafts could become a tool that agencies, corporations or even homeowners use to offset ecological damage elsewhere — an ecosystem service, Peabody said, traded like carbon credits.

“There’s a lot of discussion about whether that kind of nitrogen-trading can be achieved in Puget Sound,” she said. “This is very conceptual, and it needs to be proven and tested out in a number of environments.”

But for now, project managers are largely focused on the way an effort like this one could engage people — how it could help Islanders understand the role of shellfish and better steward Quartermaster Harbor. Last month, Peabody and Allen met with a handful of Islanders who live on Quartermaster, near where the raft will likely be anchored. There, she said, they learned about the Island’s beloved Fourth of July tradition and were admonished to make sure their raft doesn’t get in the way. But she also found a receptive audience.

Nancy Carr, who lives with her husband in the family home where he grew up on the harbor and who attended the meeting, said she and other neighbors felt an initial wave of panic when they heard about the project. “Not in my front yard, so to speak,” she said.

But after listening to Peabody and Allen describe the project, hearing their enthusiasm and learning about the community involvement that’s already begun, Carr said she now embraces the effort and plans to support it as a volunteer.

“I think it’s going to be real exciting,” she said. “Hopefully, they’ll get this harbor clean enough so that we can dig clams again like we used to.”

Gary Christophersen, another neighbor, agreed. “I think it’s a very interesting experiment,” he said.