Months after work commenced on a $30 million expansion of Coastal Maine Botanical Gardens, the Boothbay Board of Appeals on Thursday voted to rescind a permit allowing the project.

The board voted 3-2 in favor of an appeal filed by abutters of CMBG, who argued the project would further degrade the water quality of nearby Knickerbocker Lake, already listed by the state as “most at risk from new development.”

The appeals board’s decision, which followed three board meetings over several months, comes one week before the botanical gardens’ annual Gardens Aglow light show is set to begin its six-week run.

William Cullina, executive director at the botanical gardens, said the expansion was necessary to accommodate the crowds that attend Gardens Aglow each year. Last year, the light show drew 75,000 visitors.

While the board agreed with CMBG on all but one of the appeal’s points, it rescinded the permit when members voted in favor of the appellants’ argument that the botanical gardens had classified themselves as a museum rather than an educational facility — a use that is not permitted in the watershed.

In December 2016, despite loud objections by neighbors and the Boothbay Region Water District, the town’s Planning Board approved the project, which will include a new visitor center and gift shop, a restaurant in the existing visitor center, a 16,000-square-foot horticulture research and production facility, and a nearly six-story conservatory, along with expanded parking, formal gardens and trails.

But to make that happen, large swaths of wetlands — including 6.2 acres of “critical terrestrial habitat of eight significant vernal pools” — have been permanently altered.

Jodie Anthony, whose property abuts the botanical gardens, has likened a clearcut area visible from her window to “Mordor,” a reference to the dark lands ruled by Sauron, the villain in J.R.R. Tolkien’s “The Lord of the Rings.”

Anthony and her husband, Vaughn, said blasting from the first phase of the project shook their entire farmhouse. Their family pointed to critical wetlands habitat that would be destroyed by the project, although it would be offset by a mitigation plan.

Paula Ragsdale, whose house sits on Knickerbocker Lake, said construction trucks were still operating at the site midday Friday.

On Friday, Director of Marketing Kris Folsom said CMBG would return to court to “correct the Board of Appeals’ unfortunate error.”

Folsom said CMBG is pleased the Board of Appeals affirmed their project complied with the town’s zoning ordinance, but disappointed, however, that after more than a decade of permitted operations in the watershed overlay zone, some Board of Appeals members have applied a legal interpretation that CMBG is not permitted to operate within the watershed overlay zone at all.”

Folsom said the board’s decision is at odds with a February decision by a Lincoln County Superior Court Justice Daniel Billings, who declined to issue a restraining order against the town, which opponents of the project hoped would stop work until the Board of Appeals considered the matter.

At the time, Portland attorney William Harwood, on behalf of the water district, argued among other points that the gardens’ application to the town states it is an educational facility and a museum, so must meet standards for both, and museums are prohibited in the watershed.

Folsom said Friday that clarification about the purview of the board is necessary.

“We are confident that this same court will correct the Board of Appeals’ unfortunate error, but we regret the cost to the taxpayers and the community at large that will accumulate in the meantime,” Folsom wrote.

Folsom declined to comment on whether construction would continue, or whether more than 600 newly-paved parking spaces would be used for the Gardens Aglow event, “until these issues have been discussed with the town of Boothbay.”

“We will have plenty of parking for Gardens Aglow and we’re looking forward to this magical event,” she wrote. “It’s going to be quite a show.”