A massive fish kill carpeted the Shinnecock Canal, both north and south of the locks, with countless dead menhaden, or bunker, on Monday morning.

Fish kills are a natural phenomenon that occur from time to time in bodies of water and are typically caused by a lack of dissolved oxygen when a massive number of fish gather. The cause is unclear, but most believe the bunker were chased by predatory fish, like bluefish and striped bass, through the Shinnecock Inlet, up into the Shinnecock Bay and into a closed lock at the canal, where they were trapped in enormous numbers.

“I think the bunker were so thick along the beach that they came into the inlet and got trapped, because the locks were closed,” Southampton Town Trustee Bill Pell said on Monday morning. “They had no place to go—and the bluefish and striped bass hammered on them.”

Dr. Chris Gobler, a professor in Stony Brook University’s School of Marine and Atmospheric Sciences, said that in the 20 years he has lived in the area, he has never seen a fish kill in the canal.

“The canal is a confined area, and when the locks are closed, water isn’t moving,” Dr. Gobler said on Monday. “Even when there aren’t any fish in there, water is still, and the oxygen levels drop. Maybe not to fish kill levels. But when you add fish in there, that knocks the oxygen levels down even further.”

Dr. Gobler said some people, like Mr. Pell, are hypothesizing that the large number of bunker along the ocean-facing beaches that were being preyed upon by whales, dolphins, bluefish and striped bass were pushed up into the bays and tried to swim north, trapping themselves after running into the canal locks.

Populations of bunker are up this year in general, mainly because of fishing regulations imposed south of Long Island in places like Virginia, according to Dr. Gobler.

Southampton Town Supervisor Jay Schneiderman on Tuesday addressed two major misconceptions. The first, he said, is that this particular fish kill is a sign that there is something wrong with the bay or canal—but it’s a sign of quite the opposite, he said. “We’re seeing the bunker population coming back up to where it use to be,” he said. “The bunker fish play an important role in the food chain, which will help rebuild the striped bass population. It’s a positive thing.”

The second misconception is that the event is over and done with because the bluefish have migrated west—but there is still a tremendous number of bunker in the bay, he said, adding, “The worst of this may be yet to come, and that is when the dead fish come back to the surface.” The dead fish sank at around 11 a.m. on Monday morning, so many people like Mr. Schneiderman said they expect those fish to resurface starting sometime on Wednesday.

Town Trustees Ed Warner and Scott Horowitz met with Mr. Schneiderman on Tuesday morning to come up with a plan for future instances so that nobody has to scramble to get the lock opened or to clean up the dead fish.

“Right now, we’re in a period where we just have to wait and see whether the fish float to the top,” Mr. Horowitz said on Tuesday. “People are going to keep an eye on it from the air and the sea. We’re also going to keep an eye on the tides and prevailing winds.

“At this point, it’s not a public health issue,” he added.

On Monday, former Southampton Town Trustee Jon Semlear, who works as a commercial fisherman and makes a large portion of his yearly income from bunker, went to the canal to help out with the cleanup efforts, after hearing about it from a friend. Even though the fish were dead, Mr. Semlear said, they were in perfect condition for selling. “The water temperature prevented them from spoiling,” he said. “They’re great for lobster bait.”

Mr. Semlear sold the fish to Will Caldwell, who catches, buys and sells bunker to lobstermen in Maine. “Willie handled 70,000 pounds from various fishermen,” Mr. Semlear said of the number of fish scooped up on Monday. “When the locks were opened, the tide ran, and the fish dispersed. Today, I was able to get 3,000 pounds. I believe there were seven men involved in the harvesting.”

According to Mr. Caldwell, he ended up with 80,000 pounds of bunker between Monday and Tuesday, before the fish got rotten, paying the fishermen 16 cents per pound—a total payout of nearly $13,000.

Mr. Caldwell estimated that there were about five million pounds of dead bunker in the canal as a result of this fish kill.

Mr. Schneiderman said at 8 p.m. on Monday night, the canal was filled with fish. “It was literally like you could walk across it,” he said.

Worried that there would be a repeat fish kill, Mr. Schneiderman said he contacted Suffolk County officials and was able to get the lock operators to open and close the locks from 7:30 to 10:30 p.m. to not only allow the fish to move north through the canal and into the Peconics but to also help add oxygen to the water in the canal.

“It actually may have worked—they did not die off last night,” Mr. Schneiderman said.

But the fish that did die on Monday have piled up at the bottom of the Shinnecock Bay, and at some spots, Mr. Schneiderman said, they are 5 feet deep. Those fish are expected to resurface sometime soon.

Because it’s November and not August, fewer people will be inconvenienced, but when the fish do in fact resurface, Mr. Schneiderman said it’s going to reek. “There may be beaches that have massive quantities of decomposing fish,” he said. “We’re trying to figure out how to clean them up.”

Mr. Schneiderman said the fish will more than likely be taken to the Hampton Bays Transfer Station, and crews plan to mitigate the odor by using lime and wood chips.

The State Department of Environmental Conservation is going to assist in the cleanup efforts if the fish end up in marshlands. They are also in the process of testing the water and a phytoplankton sample for pathogens, nutrients and pesticides, to see if that factored into the fish kill.

As to whether a fish kill of this magnitude will happen again in the canal, Mr. Schneiderman said he doesn’t think so.

“We may not see this even happen in our lifetime, but we’ll have a sense of what worked and what didn’t,” he said.