Thousands of dead fish are piling up on the shores of the Mystic River near Assembly Row — again

Romeo Pires, of Tewksbury fished on the bank of the Mystic River strewn with dead fish. Pires, who doesn’t eat fish and only fishes catch and release was upset by the scene recounting how he saw the same thing happen two years ago.Jessica Rinaldi/Globe Staff

A malodorous stench emanated from the Mystic River in Somerville and Everett Wednesday, as thousands of dead fish stacked up on the shorelines.

The massive die-off is a scene that has replayed in these waters at least twice over the last four years, and officials say the cause, while unfortunate, is natural.

The creatures are menhaden, more commonly known as “pogies,” a fish that travels in large schools, according to Patrick Herron, executive director of the Mystic River Watershed Association. It’s likely, Herron said, that a school of the fish was driven from Boston Harbor into the Mystic by a predator, like a striped bass, or striper.

Once in the river’s shallow and warmer waters, he said, the fish probably stuck around too long and depleted the oxygen supply, leaving them to suffocate by the thousands.

“They came in in such a large school and stayed in this delimited area for so long, that they ultimately used up the oxygen in the water, grew sick, and died off,” said Herron, who has witnessed such fish kills on the Mystic River in the past.

Thousands of dead fish line the bank of the Mystic River. Jessica Rinaldi/Globe Staff

It’s the same phenomenon that plagued this section of the river in July 2018, when tens of thousands of dead menhaden washed up, creating a stench so bad that employees at a Costco that’s near the river in Everett called the city to complain.

“The smell was just terrible,” said Romeo Pires, who was fishing on the Somerville side of the river Wednesday and witnessed the die-off in 2018. “And from what I saw then, this could get worse.”

Indeed, Menhaden that are still alive in that portion of the river may wash ashore dead over the next few days, according to Herron.

The state’s executive office for energy and environmental affairs did not return requests for comment Wednesday.

In Somerville, the fish are collecting by the Amelia Earhart Dam, near Assembly Row, which features residences, restaurants, and retailers.

Dead fish were collected against the Amelia Earhart Dam in the Mystic River. Jessica Rinaldi/Globe Staff

The dead fish also washed up on the river’s shore in Everett, next to the Encore Boston Harbor resort casino.

Herron said he encountered a dense school of menhaden, which he believes to be the same school that is dying off, near the dam last Wednesday while he was boating the river.

“We saw this monster school of menhaden that went for hundreds of yards, from shore to shore,” he said. “You could look down and just see this incredible density of fish. And of course, I turned to my compatriots on the boats and said ‘Oh man, I think this will be a fish kill.’”

A school of menhaden swam in the waters of the Mystic River near the Amelia Earhart Dam in Somerville.Mystic River Watershed Association

Swarms of flies traveled from fish to fish Wednesday afternoon, and some of the menhaden that were still alive in the river appeared to struggle for breathe.

Thankfully, it shouldn’t be long before they are washed away by the tide, Herron said.

“I would counsel patience for people as they encounter them,” he said. “They will smell and then they’ll be gone.”

And while the die-off may seem alarming, officials say it’s actually a signal that menhaden are returning to the river’s waters.

“For many years Menhaden were absent from these waters due to pollution,” Mayor Carlo DeMaria said in a statement. “Today there are literally hundreds of thousands of these fish present.”

Somerville city officials did not immediately respond to requests for comment Wednesday.

Jessica Rinaldi of the Globe Staff contributed.