The Connecticut Audubon Society has joined the chorus of opposition to the Federal Railroad Administration’s plan for an Old Saybrook to Kenyon, R.I., rail bypass, sending the agency a letter Friday saying the proposed route is “fatally flawed and must be abandoned” because of the harm it would do to the lower Connecticut River estuary.

“It’s really important for environmental organizations to speak out on the impact of this,” Claudia Weicker of Old Lyme, who headed the organization’s analysis of the railroad administration’s Final Environmental Impact Statement on the project, said Monday. Weicker is chairwoman of the Board of Directors of the society’s Roger Tory Peterson Estuary Center, which is working to promote environmental education programs in the lower Connecticut River and celebrate the life of the famed author of field guides who lived in Old Lyme. The final EIS was released on Dec. 16, 2016.

The society’s letter was released on the heels of an 82-page letter from the town of Old Lyme to the FRA calling on the portion of the bypass through the town to be removed from the agency’s plan. The town’s response is critical of the proposed plans’ impact on the river, dangers to the town’s historic and artistic heritage and economy. Other towns, including Stonington, Groton and Westerly, have also criticized the plan.

Officials at the FRA could not be reached for comment on Monday.

In its letter, Connecticut Audubon is especially critical of the plan to build a tunnel under the river, a project it said would damage the fragile, unique ecosystem of the lower river. It also said the FRA’s impact statement gives inadequate analysis to the impact the project would have on threatened and endangered species in the estuary, including piping plovers, roseate terns, saltmarsh sparrows, and shortnose and Atlantic sturgeon. The National Marine Fisheries Service has designated the lower river a “critical habitat” for Atlantic sturgeon, which are federally endangered.

In addition to the harmful effects on the river, the proposed bypass would bisect several large woodlands, farmlands, and fields, Weicker said, fragmenting important habitats. The tunnel, according to the letter, would damage wetlands and tidal marshes in the Connecticut and Lieutenant rivers. The FRA, the society said, “failed to study the environmental impact of a tunnel on the estuary, its habitats and the vital functions of its wetlands.”

Weicker said the estuary center’s plan to establish an educational facility in the lower river “seems even more necessary” given the threats to the lower river from the rail project. Having the scientists and others already working with the organization to create the center, she said, “gave us a foot up on looking at the FRA report, and the things they didn’t study.”

The agency is accepting comments on the final EIS until it issues a final Record of Decision, which is not anticipated to occur before March 1. The FRA said its plan is intended to improve resiliency of the Northeast Corridor, hasten travel times, and avoid moveable bridges and at-grade crossings in southeastern Connecticut. The bypass is part of a proposed $120 billion upgrade in Washington, D.C.-to-Boston rail line.

j.benson@theday.com