Lower Yaphank Lake on Aug. 19.

Lower Yaphank Lake on Aug. 19.

Brookhaven has halted a $2.5 million project to drain Lower Yaphank Lake after discovering more than 300 cubic yards of sediment flowed into a section of Carmans River.

Town officials surveyed roughly two miles of the river flowing downstream from Yaphank Avenue after an environmental group that did its own assessment said the project had gone wrong and was interfering with the trout spawning season farther downstream.

Officials acknowledge the sediment in the river near where trout reproduce, but deny spawning was impacted.

“More sediment than anticipated” went into the river, said Brookhaven Town Chief Environmentalist Anthony Graves.

In August, Brookhaven Town began removing sediment and nonnative plants from Lower Yaphank Lake to restore it to recreational use. The town also removed the first boards from a dam to increase water flow into Carmans River. The river runs through Upper and Lower Yaphank lakes.

Town officials said they have started a cleanup project using an underwater vacuum to eradicate the silt. The removal efforts should be completed in nine days.

The New York State Department of Environmental Conservation granted the town a permit modification for the cleanup effort, but it also issued a notice of violation Nov. 6 for failure of monitoring controls in its original permit.

“DEC is closely monitoring the town of Brookhaven to address sedimentation issues caused by the lowering of water levels in Lower Yaphank Lake,” spokeswoman Erica Ringewald said in a statement. “DEC is requiring the town to remove the sedimentation in order to reduce and eliminate any threat of additional impacts downstream.”

State environmental officials said while the sedimentation is near where spawning season occurs, it couldn’t determine whether it was negatively impacted. They said spawning is currently taking place farther downstream.

But Kevin McAllister, founder of Sag Harbor-based Defend H20, on Wednesday said the sediment would have altered the conditions needed for trout to spawn. He said the fish require clean and cold water and for the bottom of the stream to be gritty in order to reproduce. Instead, the body of water has become muddy, he said.

“They [Brookhaven officials] didn’t take into account the sediments would go downstream, preventing spawning,” he said.

McAllister also questioned how Brookhaven officials measured the silt since it’s been flowing downstream for weeks.

“I don’t know how they ascertained that volume. It’s very difficult to determine the volume of silt that impacted the stream,” McAllister said.

He added that cleaning crews removing the silt have also disturbed the spawning season, which runs from mid-October through November.

On Friday, the environmental group along with state DEC officials and town officials met over the issue.

The group said it requested all county and state permits in relation to draining the lake and the river remediation efforts but only received partial information.

McAllister said he wants to ensure town crews aren’t discharging the silt into nearby wetlands.

Officials estimated that the Lower Yaphank Lake project would cost between $2 million and $2.5 million and was scheduled for completion in May.

The project timeline included scraping the lake bottom this winter to remove nutrients that feed the invasive plants.

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