A $1.95 million dredging project planned for the Menemsha channel may be dead in the water after the Chilmark selectmen pulled their support for the project this week.

Funded by the Army Corps of Engineers, the project called for dredging six feet from the Menemsha Basin through the creek and into the pond. Funds were allocated as part of the $50 billion Hurricane Sandy relief bill in 2012. The corps said the dredging will improve navigation in the channel where some areas are as shallow as two or three feet due to shoaling.

The project was slated to start next fall and follows nearly a year of planning and studies among the towns of Aquinnah, Chilmark and the Wampanoag Tribe of Gay Head (Aquinnah). The pond basin lies in both towns.

On Tuesday the Aquinnah selectmen voted to green light the project, citing benefits to navigation and lauding a plan to use the spoils to restore dunes at Lobsterville Beach.

But at their meeting later the same day, the Chilmark selectmen put the brakes on the project after hearing concerns from town shellfish constable Isaiah Scheffer and harbor master Dennis Jason.

“If I’m acting in the best interest of Chilmark and shellfish, I would recommend not to dredge the channel,” Mr. Scheffer said. He said the shellfish committee also did not endorse the plan. “One of the things is there are going to be larger boats in the pond [once the channel is deepened] . . . it would take a lot of enforcement,” Mr. Scheffer said.

Mr. Jason agreed. “As a fisherman I’d rather see it not dredged, as a harbor master it will cause us more grief patrolling,” he said. “I don’t know what that’s going to do with the Chilmark side of [shellfish] propagation, which is more important to me and generations coming after.”

Selectmen joined the opposition. “I’m very much with the shellfishermen and not in favor of this,” said Jonanthan Mayhew. “I think we should take the slow route and not worry about what the funding is. The funding is there but there are a lot more people in New Jersey that need it more than we do.”

Selectman Bill Rossi was also skeptical.

“All I’m hearing is from the shellfishermen who all seem to be against the project,” he said. “I’m trying to look at the whole town and a lot of people have access to the ponds . . . but none of them have spoke up or said anything. I don’t have a lot of confidence in this.”

Longtime resident Everett Poole echoed concerns about easing the way for larger boats to enter the pond.

“I would hate to see Menemsha Pond become a mooring facility, which I’m afraid it would,” he said. “It’s good to get some circulation there . . . but I don’t see opening up the present channel straight through, that’s just going to fill the place with yachts.”

Bret Stearns, natural resources director for the tribe, had a different view. He said studies preparing for the project show it will benefit shellfish.

“I’ve invested in studies to find out the right answer . . . if they came back and said it’s not looking good for scallops, it would have been a no brainer for me,” Mr. Stearns said.

But Mr. Scheffer said if a large storm brings more sand into the channel, dredging can be done then.

Mr. Stearns replied: “It is going to be on the community to pay for it. This is the first time I’ve seen relief in this fashion in 20 years.”

On Wednesday, Mr. Stearns said he was disappointed in the outcome.

“There was a great amount of technical information which led us to the conclusions that there would be no negative impact to shellfishing, which was the primary concern of the tribe,” he said. “I remain concerned that the current depth of the channel could restrict flow into the future and that would have severe impacts to the pond and the entire pond system.”

Craig Martin, Army Corps project manager for navigation in the New England district, said Wednesday that his team is deciding what the next step should be.

Meanwhile, a jetty repair project will go forward at Menemsha, he said. The $1.5 million project will involve repairs to some of the large armor stones that were damaged during Hurricane Sandy.

“We’re going to bring it up to the code it was built to,” he said.

Construction on the jetty is expected to start next December.