An estimated 300,000 bunker have since gone belly-up in the river or washed up along its banks, local experts said. Schools were still trapped up river and dead fish dotted the shoreline nearly a week later, setting the stage for a stench that could linger in the downtown area for days to come.
"The kill numbers have greatly increased as the week progressed," said Bob Conklin, a former marine biology teacher who surveyed the river with a team of experts Monday. "This is going to be a royal mess for Riverhead. These dead fish are just going to be moving back and forth with the tide."
The massive school began to infiltrate the Peconic last Wednesday night, drawing fishermen from miles around. By last Thursday, it was a river of fish.
It took George Yakaboski and his son, George Jr., both of Riverhead, just 45 minutes to scoop up 700 pounds worth of bunker from the river last Thursday behind Main Street.
"Half of it we'll use for shark chum and the other half for bait," said the elder Mr. Yakaboski, a recreational fisherman, after packing 10 crates of fish into his pickup. "They were actually suffocating themselves and jumping on the shores."
Fishermen also lined the riverbanks downstream, where they were using chunks of the bunker to catch a seemingly endless number of bluefish from under the Route 105 bridge.
"I've never seen anything like this before. It's like fishing in a tank," Brian Bragg, 21, of Holbrook, said between catching and releasing large blues under the bridge.
While a spring migration of bunker up the Peconic River and other area tributaries isn't unusual, the enormity of this school made for a spectacular event.
"I've lived here 30 years and I've never seen that," said Bob Kent of the New York Sea Grant research group. "It was like you could walk across the water on the fish. It was unbelievable."
According to Aphrodite Montalvo, a Department of Environmental Conservation spokeswoman, "This does happen every year and sometimes we have smaller kills. This was just a larger school. They spawn, traditionally, south of here and make their way up the marine district in search of food.
"In this case they found themselves in the narrow confines of the Peconic River and got trapped by bluefish," she said.
Mr. Conklin said he went to the river last Wednesday night to fish for striped bass when he noticed the bunker run.
"The blues herd the bunker," he said, explaining the dynamic that led to the influx in the river. "You see the shorelines, and the water just explodes because those blues push the bunkers right up against the shore. They herd them into a shallow area where they're easy to nail."
Many of the bunker fish seen swimming alongside the riverfront park boardwalk last week had chunks of flesh ripped off them and some were bleeding, the apparent result of run-ins with the blues.
They fared no better upriver, due to a combination of low oxygen levels and fresh water, said Mr. Conklin.
"They can only live about eight hours in fresh water," Mr. Conklin said. "And a big school of bunker like that can drain oxygen from the water pretty quickly."
Since the migration was part of a natural life cycle, Ms. Montalvo said there was nothing DEC workers could have done to free the fish.
"I wish there was some way you could scare them and get them back up the water and out of there," said Frank Rizzuto, 64, of Riverhead, who was walking along the riverfront last Thursday with his wife. "I actually feel sorry for them. If you look at them it looks like they're not breathing properly.
"That's an incredible scene," he continued, squinting over the normally placid river, suddenly alive with a combination of shiny, flapping fins and floating white underbellies. "That's really unbelievable."
Suffolk County health department workers were also out on the water last week. Marine bureau personnel found depressed oxygen levels from the Route 105 bridge to Atlantis Marine World, officials said.
"The bottom waters off Atlantis had no oxygen at all, so there was a serious situation there," said Mac Waters, who heads the marine bureau. "At the surface the water's closer to the atmosphere, so there's more oxygen. That's why they were all congregated at the top."
Bunker, officially known as menhaden, of the herring family, grow to about 12 inches long and are found primarily in northeastern waters. An oily and bony fish, they are most often used as bait for bluefish and striped bass or ground into chum for shark expeditions and fertilizer, area fishermen said.
Some people, however, make them into a meal. One Riverhead resident, Pearl Higgins, 51, who was at the park Thursday afternoon packing plastic bags with bunker, said she was planning an old-fashioned fish fry with her catch.
John Blakes, 37, also of Riverhead, said he used his 10 bunker to reel in 12 hefty bluefish from under the bridge.
"I'm filleting some and I'm going to give some to my family," he said of the bluefish. "I either broil them or grill them. They're good."
A single bunker usually fetches between $1 and $1.50 at area bait shops, which also got their share of calls from people looking to turn a quick buck.
"They keep calling and keep calling, and I keep saying, 'No, no, no," said Ed Kopack, the owner of Warren's Tackle in Aquebogue. "I don't have the capacity to put it away."
Although Riverhead Town's bay constable, Jim Divan, was confident the fish that died would be swept out to the bay rather rapidly, he added that the kill count could rise as the days passed.
In the meantime, the only thing to do is wait and see, he said.
"I haven't had this experience in the Peconic River since I've been here," he said. "You know what's going to really smell? The ones that get trapped underneath people's floating docks," he said, noting the warming temperature trend this week.
"It could be a mess," he said.