A fish kill of major proportions is underway in the Peconic Estuary and as marine researchers are sampling the water for further study, town officials are working to prevent it from becoming a public health hazard.

Tens of thousands of fish in the bays, creeks and river have died due to lack of oxygen, according to Dr. Christopher Gobler of the Long Island Coastal Conservation Research Alliance and a research professor at Stony Brook University’s School of Marine and Atmospheric Sciences.

Gobler says a “massive mahogany tide” — the algae Prorocetrum — is blooming in the estuary. The bloom began in early May. Levels of Prorocetrum in water samples tested by researchers are “some of the highest we’ve seen in the region,” Gobler said.

The algal bloom is “driving the oxygen levels down, which is leading to anoxia and the fish kill,” he said.

“Dissolved oxygen levels dropped to zero for an extended period” Thursday night, Gobler said on Friday.

“Yeah, well everybody has their own theory,” Riverhead Supervisor Sean Walter said this morning, when told of the scientist’s assessment. “Mine is that the bluefish are chasing them into the river.”

Bunker fish kills in local creeks and in the Peconic River are not uncommon in the area when bluefish are running in spring. The blues chase schools of bunker — thousands of them — up the river or up a creek, where they become trapped. The volume of fish combined with low tidal flushing in these areas drives oxygen levels down and the fish die. A large bunker die-off occurred in May 2009 in Meetinghouse Creek and the Peconic River.

Gobler said today the current die-off is likely the largest in decades and significantly larger than the 2009 Meetinghouse Creek. The current fish kill in the bay is the largest he’s ever seen, he said.

Harmful algal blooms, such as the mahogany tide — as well as the red tide, which may be responsible for the recent turtle die-off — are caused by excessive nutrient and nitrogen loading in waterways.

Dead bunker accumulated on the shore of Flanders Bay west of Simmons Point in Jamesport shortly after low tide early this morning. Yesterday’s high tide line was marked by piles of dead fish, stretching out as far as the eye can see. Dead fish — mostly bunker and a few blues — were coming in with the rising tide. The smell of dead fish was already noticeable on Peconic Bay Boulevard.

Dead fish were floating in the Peconic River along the downtown waterfront this morning in numbers that caught the attention of passersby and visitors to the outdoor farmers’ market on the boardwalk.

The town supervisor, who late yesterday said he hoped fishermen could use nets to pull live fish out of the water in quantity before they die, today said he’d given up on that idea.

“Obviously we need to think cleanup,” Walter said in a phone interview today. “We need to make sure this doesn’t become a public health hazard.”

The supervisor said if he needs to declare a state of emergency to get the cleanup done and dispose of the fish, he would do so. Walter said he is looking into burying the dead fish at either the Brookhaven town landfill or Riverhead’s long-closed Youngs Avenue landfill. He said he was not sure if the town would need permission from the state Department of Environmental Conservation in order to bury the fish in either place. The DEC’s Region I director Peter Scully recently left the agency for a position with Suffolk County and Walter said he was unable to get in touch with the acting regional director.

“I think a declaration of a state of emergency would cover us,” Walter said. “I’ve asked the town attorney to research it and draft it today. ”

At the downtown dock late this afternoon, Walter said he is grateful for the strong winds which, he said, are helping to move the water — and the dead bunker — out of the river more quickly. “I think this may have helped us dodge a bullet,” he said.