Nashaquitsa Pond has become a laboratory for eelgrass restoration, although poor water quality and other factors appear to be keeping the aquatic species from re-establishing in areas where it flourished just two years ago.

Following a harsh winter in 2015, almost no eelgrass returned in the pond, confounding Chilmark shellfish constable Isaiah Scheffer and others, especially since the eelgrass in Stonewall Pond to the south and Menemsha Pond to the north was still relatively abundant. EPA biologist Phil Colarusso surveyed the site last summer and pointed to crab and goose foraging during the winter as likely causes of the decline.

This spring, Mr. Scheffer launched a yearlong eelgrass restoration project with funding from the Edey Foundation and additional support from the town of Chilmark. The project is still in the early stages, but the results so far indicate an uphill battle.

A wasting disease in the 1930s wiped out about 90 per cent of the eelgrass along the East Coast. Some of it grew back, but with declining water quality, the population is only a fraction of what it was. Nearly all the eelgrass on the Cape has disappeared as a result of increased nutrient loading, which leads to algal blooms that deprive pond organisms of light and oxygen. Vineyard ponds are in much better shape, but still face an uncertain future as development continues in the watersheds.

Eelgrass plays a vital role in coastal ecosystems, providing food and habitat for many species, and aiding in the process of sedimentation. Its high sensitivity to water clarity also makes it something of a canary in the coal mine when it comes to the health of coastal ponds. The Massachusetts Estuaries Project uses eelgrass as a primary measure of habitat restoration.

Not surprisingly, reestablishing the species depends largely on water quality. Some argue that restoration should focus entirely on water quality improvement, while others take a more comprehensive approach.

In Chilmark, the efforts combine a number of techniques, including planting salvaged shoots and collecting flowering stalks to reseed the area. The project takes a low-impact approach, using biodegradable burlap and only planting those shoots found floating on the surface in nearby ponds.

A few buoys are visible from the shore, each one holding five mesh bags filled with flower stalks that will release their seeds over the course of the summer.

The project builds on a method known as transplanting eelgrass remotely with frames, or TERF, which was pioneered by University of New Hampshire professor Fred Short in the 1990s.

Unlike the original TERF method, the Chilmark project involves the use of burlap, rather than paper ties, to hold the plants in place. Each eelgrass shoot is threaded through the burlap and the entire frame is anchored to the bottom with rocks and sediment.

“You look at it and you’re like, okay this is going to work,” Mr. Scheffer said this week. But so far the method has seen only about a five per cent success rate, with most plants dying within a week.

“Turbidity is definitely still playing a big role,” Mr. Scheffer said. The first 10 frames — each one measuring three by six feet — have served as a trial, while 40 others remain to be installed.

But with limited success so far, Mr. Scheffer is beginning to rethink his approach. He plans to retest the method alongside the existing beds in Menemsha Pond. “If [the plants] die after we do that, then we realize that what we are trying to do is just not going to work,” Mr. Scheffer said.

The project also involves the use of rocks to anchor larger clumps of eelgrass to the bottom. But so far those are no better than the modified TERF approach. Mr. Scheffer was still holding out for the seeding method, known as buoy-deployed seeding. Each mesh bag contains thousands of seeds.

But methods are only part of the equation.

“Having the right site is critical,” said Mr. Short, speaking to Gazette by telephone on Wednesday. “If the water clarity isn’t good, if there’s some disturbance going on — clammers coming through or something — then no method is going to produce a viable bed.” He added that areas with adequate water quality, where eelgrass still grows, usually have the best results.

Oak Bluffs shellfish constable David Grunden said previous efforts to restore eelgrass on the Vineyard have also failed. He recalled attempts to transplant and reseed eelgrass in Sengekontacket and Lagoon ponds a few years ago, but the new shoots came under attack from crabs. In response, the town covered them with netting, which blocked out even more sunlight.

“We have to improve the water quality before we can get the eelgrass to come back,” Mr. Grunden said this week. But improving the water quality even in the less impaired ponds will likely require a variety of methods over many years, and a new level of cooperation, since most major watersheds on the Island cross at least one town boundary.

A recent proposal by the Tisbury board of health to introduce a nitrogen tax for new developments in the Lagoon and Tashmoo Pond watersheds has drawn fierce opposition. Other efforts to mitigate the amount of nitrogen entering the ponds, and removing the nitrogen already in the water, are slowly taking shape but will also depend on public support.

In general, the success of eelgrass restoration along the coast has hinged on water quality. Clear water was key to restoring thousands of acres of eelgrass in Virginia’s seaside lagoons beginning in the late 1990s, while restoration in Chesapeake Bay has been challenged by higher temperatures and turbidity. Restoration efforts in Narragansett Bay fell short of the goal, but improving water quality may provide a new window for the species to take hold.

Robert Orth, a leading seagrass expert at the Virginia Institute of Marine Science, said the shallower and cooler water, along with constant circulation allowed a long-term seeding program to restore vast eelgrass beds in Virginia’s seaside lagoons. Biologists and volunteers reseeded about 500 acres of eelgrass meadow over the years, with the population naturally expanding to cover an additional 5,600 acres.

It was a different story in Narragansett Bay, where long-term restoration efforts by the group Save the Bay were hampered by nutrients from runoff and groundwater. The project started in 2001 using the TERF method, later switching to hand-planting, which was more labor intensive, but also more successful. But none of the sites in the northern bay, where nutrient levels were highest, produced viable beds. The project ended around 2012.

At the same time, however, Save the Bay and other groups have succeeded in greatly reducing the amount of nutrients entering the bay through wastewater and runoff. Biologist Tom Kutcher of Save the Bay noted a 50 per cent reduction over the last 10 or 15 years and hoped it would open the door for more eelgrass in the bay.

The group has also worked to restore bay scallops, which would further clean the water by filtering out phytoplankton, and it is working to improve water quality in the upper bay by introducing ribbed mussels. (A shoreline restoration project underway in Sengekontacket may also involve the seeding of ribbed mussels to help reinforce the bank and filter the water.)

The TERF method may still prove to be the best approach for Nashaquitsa Pond, since it seems to work best in small ponds water with gentler currents. “If the grass was there and it was lost because of some physical damage, it should be all right,” Mr. Short said. But he questioned the modified TERF method in use, since burlap tends to flap around in the current, even with a frame around it. “The plants aren’t going to root if they are moving,” he said. “They’ve got to be kept steady in place.” He added that burlap may attract crabs, which like to nest under solid objects.

In the traditional TERF method, shoots are tied to a metal frame with paper strings. After about a month, the strings and frames are removed, leaving only the eelgrass. Mr. Scheffer planned to mitigate the problems with burlap by pouring sediment over the frames. After the plants take hold, he would cut away the burlap or to let it biodegrade over a period of about two years.

Mr. Orth said the process of casting seeds from boats happened to be the easiest and most effective solution for the Virginia lagoons. But he highlighted the importance of water quality for all restoration methods.

“Anything works,” he said. “TERF, individual shoots, shoots with anchors, double shoots, coirs, mats, you name it. We’ve tried it all. They all work if there’s good water quality.”

Mr. Scheffer’s project includes money for underwater cameras that could help refine the project and shed light on why the eelgrass suddenly disappeared last year. He believed crabs may be partly to blame, but he wanted to rule out other possibilities. Many questions remain, he said, including whether the salvaged eelgrass is healthy enough to replant.

Mr. Colarusso, the EPA biologist, plans to return next week and provide additional guidance.

“I expected more survival of the shoots,” Mr. Scheffer said, but he wasn’t surprised that the project was off to a shaky start. “There is a reason why none of this is easy,” he said. “If it was easy, then it we wouldn’t have a problem with eelgrass.”