The director of the Martha's Vineyard Shellfish Group said yesterday that nearly four million healthy juvenile shellfish under culture at his Lagoon Pond hatchery have died in the last three weeks because of extremely poor water quality in the pond.

The deteriorating water quality has not affected mature shellfish and there is no danger to humans who eat shellfish from the pond.

But hatchery director Rick Karney expressed open anguish at the titanic shellfish kill in the hatchery this week, and he said bluntly that he believes a crisis now looms for the ponds of the Vineyard, which have historically been pristine and rich with shellfish.

"I have been here 27 years and I have never seen water quality as poor as it is this year. I have never seen anything like this ever before," said Mr. Karney, a veteran marine biologist who has run the shellfish hatchery on the Lagoon since its inception as an experimental program nearly three decades ago.

The hatchery relies on water pumped directly from the Lagoon for its program.

The Lagoon Pond hatchery is now at the height of its season and was nurturing about a million baby oysters and three million baby scallops. Mr. Karney said more than 90 per cent of the shellfish have died in the last three weeks. William Wilcox, the water quality planner for the Martha's Vineyard Commission, and Oak Bluffs shellfish constable David Grunden went out on the Lagoon early this week and documented two large areas of the pond where the oxygen levels were extremely low. An absence of oxygen in the water creates a condition that is termed anoxic; marine life depends on oxygen in the water for growth and survival.

These two large areas - stretching from the deep water in front of the hatchery to the extreme southern end of the Lagoon - tested as what scientists call "dead water." No marine life can survive in dead water; if the condition persists, the wider effect on the health of the pond is unknown. Fish can move around a pond by swimming, but shellfish are relatively sedentary and depend on oxygenated water that comes from good circulation.

For now, Mr. Wilcox said that while the direct cause of the shellfish kill at the hatchery is not yet known, there is little doubt about the connection between the anoxic water and the die-off.

"It's highly likely that some microscopic organism grew to excess and caused the trouble in the hatchery. And it is very likely that the anoxia or near-anoxia conditions contributed to the growth of this organism," Mr. Wilcox said.

This week Mr. Karney's distress was compounded when he learned that a separate problem had erupted at the shellfish group's satellite hatchery on Chappaquiddick.

Some eight million healthy, maturing quahaugs had been moved last week to this hatchery, on the outer Edgartown harbor. After about half of those had been distributed to five of the six Vineyard towns for planting in ponds (West Tisbury has no quahaug fishery), the remaining quahaugs in the hatchery began to die suddenly after the July Fourth weekend.

Mr. Karney is investigating the cause, but he said he believes the die-off may have been caused by discharge from boats anchored in the outer harbor.

"I heard the Edgartown harbor was like a city full of boats," Mr. Karney said. "I can't say for sure but it is probably something toxic in the water because disease doesn't kill shellfish that fast," he said.

Last summer the Chappaquiddick hatchery had a bad scare and nearly lost a million quahaugs after a mysterious oil spill fouled the intake water in the facility.

Yesterday Mr. Karney chronicled the events in the Lagoon this year, which have a number of components, including bad weather, poor circulation in the pond and the possible growing presence of dinoflagellates, a phytoplankton that is in the same family as red tide.

A study done in the Lagoon last summer detected the presence of some dinoflagellates.

But last summer the conditions were dry and sunny.

This year the conditions have been wet and rainy.

Heavy rain introduces nutrients into the pond, both from acid rain and from groundwater discharge. Nutrients stimulate the growth of algae and cloudy weather sets the stage for the algae to die, leading to anoxia. Shellfish need nutrients from the water in order to grow. But too many nutrients cause large algae blooms, depriving the water of oxygen and starving the shellfish. In the anoxic cycle, phytoplankton "rain" down to the bottom of the pond, creating a dead bottom and leaving the organisms on the top layer struggling to survive.

"Three weeks ago it rained heavily on the weekend and after that everything crashed. We had all this organic material, our tables were teeming with organic material," Mr. Karney said.

The shellfish began to die.

"We have been working seven days a week for five months, and to see it go down the tubes as fast as it has is just devastating," Mr. Karney said. "This is a water quality issue that is affecting the shellfish resource - I have serious doubts that if this kind of situation continues whether we can even run this facility. We can't continue to do our job. This is the stuff that's in the Gulf of Mexico - when you have anoxic bottoms the fish go belly-up," Mr. Karney said.

Mr. Karney met with his board this week to discuss the problems. He said studies done on the pond in recent years have pointed to the need for some dredging, and he said the need is now acute.

Mr. Wilcox agreed that strategic dredging would help to improve the circulation in the pond. He said the Lagoon flushes only about once every ten days or two weeks. By contrast, Sengekontacket Pond flushes every two or three days.

But Mr. Wilcox said dredging is only one part of the solution; he said more work needs to be done to fix a firm nitrogen loading limit for the lagoon. A recent study by the commission found that the pond is at its limit for nitrogen loading.

"It is based on reasonable scientific information but it needs to be more thorough, and we need to address nitrogen loading from the watershed before buildout. It's a painful process, but it needs to be done," he said.

Mr. Karney, Mr. Wilcox and Mr. Grunden said they are also concerned about the recent proposal by state highway officials to build a temporary drawbridge alongside the present drawbridge. The project calls for some filling around new buttresses planned for the inlet beneath the drawbridge, which Mr. Karney and Mr. Wilcox said will impede the circulation in the pond even more.

"We are totally flipped out about that," Mr. Karney said of the drawbridge plan.

The Lagoon Pond hatchery began as a pilot program in 1978 and the permanent solar hatchery opened in 1981. The Chappaquiddick hatchery opened in 1995. The hatchery program has produced an average of 20 million shellfish seed every year, including quahaugs, oysters and scallops. The seed is distributed to the six Vineyard towns. The annual budget for the hatchery program is about $150,000; a good portion of it is grant money.

The return on the dollar for the program is excellent: The shellfish industry in the six Vineyard towns was valued at more than $3 million last year, based on numbers published in the annual town reports. Mr. Grunden said in Oak Bluffs alone the shellfish crop last year was valued at about $1 million. "And that was an average year for scallops. In a good scallop year the number is much higher," he said.

Ironically, by most accounts the adult scallop set in the Lagoon this year looks healthy and Mr. Grunden said he expects a good year. But it is not known what effect the poor water quality will have on the wild juvenile scallops.

Mr. Karney said his hatchery is the canary in the coal mine.

"We are here weekends and holidays and we love our work and we have the satisfaction of producing these animals - but if we're going to continue this program we are going to have to address these issues. I am working for the fishermen - we don't want to scare people, but really we have a huge water quality problem here. We are working with the small and tender animals and they are the first ones to go. People ask, why don't we have scallops like we used to - well, if this is happening in our facility it must be happening to some degree in the wild," he said.

Mr. Karney said he has relied on the Chappaquiddick hatchery as a place to move the quahaugs during the summer months, as the water quality problems in the Lagoon have increased. "And now the Chappy situation seems to be getting chronic," he said.

Recently the hatchery has been experimenting with breeding triploid oysters, a project that involves growing shellfish with an extra set of chromosomes to make them sterile and resistant to disease.

Mr. Karney concluded:

"When I left the meeting last night my board said ‘Spawn and spawn again.' - we've got another 10 million oysters to do and we're trying to keep our heads up and do it, but it's not easy. We can't continue like this. We can't keep putting in this effort to have these kind of losses. I am so frustrated I am ready to throw in the towel. Our program is in jeopardy."