Rapidly rising water temperatures, the timing and magnitude of algal blooms, and an unusually large amount of frightened fish in one location led to alarmingly low levels of dissolved oxygen in the Peconic River, causing three fish kills last year, researchers found.

The deaths of nearly 300,000 Atlantic menhaden — commonly known as bunker — reflect the need for a collaborative effort to improve the river’s water quality, acting DEC Commissioner Basil Seggos said.

“We will be on the lookout this coming summer for a similar confluence of factors,” he said in a statement.

Suffolk officials blame excess nitrogen for the growth of harmful algal blooms. Some $364 million in state and federal recovery aid will be used to improve sewer infrastructure in Suffolk in an effort to stem nitrogen pollution and bolster coastal protection.

Peter Scully, deputy county executive for administration, said Suffolk already is testing measures to improve cesspools and could ultimately mandate their replacement.

Investigators with the Suffolk County Department of Health Services, New York State Department of Environmental Conservation, Cornell University and Stony Brook’s School of Marine and Atmospheric Sciences — which conducted the study — found normal levels of nutrients, bacteria and pesticides in the water, discounting the possibility of illegal discharge, spills or the presence of toxic substances.

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They say pathology reports indicate the fish died from asphyxiation.

The bunker also had gill damage caused by exposure to harmful algae.

Evidence of a virus was found but it is not clear to what extent it contributed to the deaths.

The Peconic has a long history of degraded water quality, the researchers said, but 2015 was unique in that spring algal blooms were “more intense” than in previous years and the oxygen decline in the water happened much sooner.

“As temperatures increased in the spring, all that was needed was a large body of panic-driven menhaden trapped by predators to finish off whatever oxygen was left,” the report said.

Christopher J. Gobler, a professor at Stony Brook University who contributed to the study, said waste water-related improvements will reduce the likelihood and magnitude of future die-offs.

“There will be less nitrogen . . . going to the river, which will minimize intensity of future algal blooms and oxygen stress on that system,” he said.

The first 2015 die-off, on May 16, was relatively minor. Hundreds of thousands of fish died in the second instance, on May 27.

Another 10,000 bunker expired June 14.

Kills also were reported in the Hudson River, New Jersey, Connecticut and Rhode Island.

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In addition to monitoring sites within the river itself, researchers examined several other locations, including Meetinghouse Creek, Terrys Creek and Sawmill Creek. They tested them for salinity, temperature, dissolved oxygen, coliform bacteria, nitrogen and phosphorous nutrients, as well as organic solvents, pesticides and radiological residues.

South Jamesport bathing beach also was checked.

Samples in early June showed a lack of dissolved oxygen at toxic levels at mid-depth and bottom waters of the river from the Moose Lodge to Riverfront Park, researchers said.

Better flushed water to the east — including the Peconic River mouth, Reeves Bay and Flanders Bay — had greater oxygen level but were not optimal.

All other tests revealed results in the normal range.