A clogged overflow drain on Lily Lake, also known as...

A clogged overflow drain on Lily Lake, also known as Lower Lake, one of a pair of man-made ponds in Yaphank created centuries ago to serve grist mills. Credit: Daniel Goodrich

A Sag Harbor-based environmental group said it plans to sue Brookhaven Town, Suffolk County and other entities over a dredging project on the environmentally sensitive Carmans River.

Defend H2O said the dredging of Lower Lake in Yaphank, intended to improve water flow and restore natural habitats, damaged spawning areas for brook trout further down the river before state authorities halted the project late last year. Dredging has not resumed on the lake.

Kevin McAllister, Defend H2O president, said that on Thursday the environmental organization filed a notice in federal court of its intention to sue the town, Suffolk, the state Department of Environmental Conservation and the state Pine Barrens Commission. He said the suit would claim that the dredging project violated the federal Clean Water Act and other federal and state environmental protection laws.

Specifically, the town and county failed to obtain permits from the Army Corps of Engineers, and the DEC and pine barrens commission did not properly enforce their own rules, McAllister said. The lawsuit will be filed within two months, he added.

“We certainly want the project stopped until proper permitting is completed,” McAllister said in an interview, adding that he hoped to speak to Brookhaven and Suffolk officials about altering the project to protect wetlands. “It would revert back if conditions are changed to support recolonization.”

Brookhaven, DEC and pine barrens officials declined to comment. A county spokesman did not  return a call and email seeking comment.

Brookhaven has sought for years to remove invasive plants and other debris from Yaphank's Upper and Lower lakes, a pair of man-made ponds created centuries ago to serve grist mills. The town cleaned Upper Lake several years ago.

Brookhaven last summer began a $2.5 million effort to drain Lower Lake, also known as Lily Lake, and scrape its bottom with heavy equipment. It was halted in November by the DEC, which found the town had failed to implement required monitoring systems and control turbidity, or cloudy water caused by excess sediment. Town and DEC officials are in talks to revise the project to meet state standards.

The DEC acted after state and town officials said more than 300 cubic yards of sediment had flowed into a section of Carmans River where brook trout typically spawn.

Despite the state decision to stop the project, McAllister said the DEC had not followed its own rules regarding turbidity when it approved the project two years ago. McAllister has said the lakes should be removed so that the river's natural flow can be restored.

“What the state did was assign standards that were more relaxed than their own standards,” McAllister said. “It was a bit arbitrary on their part on what they allowed.”

Town officials have said they are working with engineers to design a different system for removing invasive species from the lake.

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