Due to high bacteria counts, the state Division of Marine Fisheries closed portions of two large Island ponds to shellfishing this week - one up-Island and the other down-Island.

The closures are effective immediately in part of the Tisbury Great Pond and at Major's Cove in Sengekontacket Pond, although town leaders have not yet received official letters of notification.

This marks the first closure for the northern section of Tisbury Great Pond, which spans Chilmark and West Tisbury. The closure includes Town Cove, which tested above state recommended levels for fecal coliform bacteria twice in a 14-month period. The state has now placed the northern portion of the pond on what is termed status closure, which means more than 10 per cent of the water samples taken for testing in the last three years have exceeded the state minimum for fecal coliform counts.

Mike Syslo, a senior marine biologist for the division of marine fisheries and former director of the state lobster hatchery in Oak Bluffs, said this week that he is less concerned about the Tisbury Great Pond closure and more concerned about the closure at Sengekontacket.

"I'm very uncomfortable with what's happening in Sengekontacket," Mr. Syslo said, noting that bacteria counts all over the pond seem to be rising, even if they remain below minimum state thresholds. "I'm probably going to be sampling that pond more often than is required," he said.

Mr. Syslo tests water quality in all of the Island ponds five times a year, and every January he analyzes the numbers according to federal regulations. The closures this week are the result of that analysis, although the last water samples that tested high for fecal coliform were taken months ago.

Mr. Syslo said the high counts at the Tisbury Great Pond could likely be traced to waterfowl. "This could have been something as temporary as a flock of geese on the cove that I didn't see before I got there," he said. "It's not something I'm terrifically concerned about," he added.

The closing of about two thirds of Major's Cove in Sengekontacket is more ominous, Mr. Syslo said. The cove, which is shared by Oak Bluffs and Edgartown, harbors beds of quahaugs and bay scallops, but has been on status closure for the last couple of years. Now most of Major's Cove will be reclassified as a prohibited shellfishing area. As a prohibited area, it would take a minimum of three years of low bacteria counts and cutting through a maze of red tape to reopen that part of the pond, Mr. Syslo said.

In addition, a 100-foot area around Haystack Point in Edgartown, toward the southern end of Sengekontacket Pond, was placed on status closure for the first time.

The minimum state threshold for fecal coliform is 28 colony-forming units per 100 milliliters.

Colony counts over 50 are not detailed but simply reported as greater than 50 by the lab. Major's Cove has received several of these readings in the last few years - ruling out the possibility that the high readings are simply a fluke caused by flocks of waterfowl.

Mr. Syslo said he expects the economic impact of the Sengekontacket closure to be greater than in Tisbury Great Pond - and he believes it will affect Oak Bluffs more than Edgartown, which has significantly more shellfishing acreage in Katama Bay and at Cape Pogue Pond.

"As of right now, no one is shellfishing that neck of [Tisbury Great Pond] anyway," Mr. Syslo said of the Town Cove area, which is open to shellfishing seasonally from Nov. 1 to April 30. "We didn't feel economically it was going to impact any shellfishermen."

The closure in the Tisbury Great Pond runs from just north of a sandbar called Big Sandy on the Chilmark side of the pond, to Plum Bush Point on the West Tisbury side. Shellfishing is already prohibited in the northernmost parts of the coves, where the water is shallower and the circulation lower.

"As you go farther north to the far reaches of the pond, the water quality typically gets worse,"  Mr. Syslo said, noting that Big Sandy partially obstructs the opening to Town Cove. "It cuts off a lot of circulation to the upper half of the pond," he added.

With little development around Tisbury Great Pond, Mr. Syslo said he is not concerned that the high fecal coliform readings are coming from septic system discharge.

"There's only two cottages in that whole area," he said. "I'm convinced it's just lack of circulation and a lot of waterfowl on the pond."

But West Tisbury shellfish constable Thomas Osmers said he is concerned by what seem to be increasing bacteria counts overall in the pond, in addition to other conditions that are damaging to the shellfish, rather than the people who eat them, such as dermo, a disease that affects oysters.

"Usually this is something that would happen in summertime," Mr. Osmers said of the pond closure. "The fact that it's happened here in winter cannot be a good sign."

He said it is sad news for towns that have been struggling with other shellfishing issues.

"We've been already showing problems," Mr. Osmers said. "Growth of algae, low oxygen events in parts of the pond, degradation of the marine environment. We've had a great amount of clams every year - millions of them - enough to support seven or eight fishermen. Now every year the clams die, which is the sign of a stressed marine environment."

In positive news for Sengekontacket Pond, the state has lifted a status closure in an area just outside Trapps Pond, which connects to Sengekontacket on the extreme eastern end in Edgartown. Mr. Syslo estimates that the area covers roughly three acres. It will now be up to town officials to reopen the area to shellfishing.

The news of pond closures this week comes amid increasing discussion on the Vineyard about declining water quality in the coastal ponds and study work aimed at pinpointing the source of pollution. In Edgartown the board of health has placed a septic moratorium on a large residential area in Ocean Heights that runs until March, while it conducts a study of the area. Meanwhile, across the Island coastal planners and shellfish biologists are waiting for the first results of the Massachusetts Estuaries Study.

Mr. Syslo said despite the concerns, Island ponds are in comparatively good health.

"In the overall picture statewide, it's unbelievable how blessed we are here on the Vineyard with clean water," he said. "But still, you've got to remain vigilant."