A project to rebuild the two jetties at Menemsha harbor is expected to begin in the next two weeks, while a more controversial project to dredge the channel to Menemsha Pond has been delayed until next fall. Both projects will be handled by the Army Corps of Engineers.

The harbor’s west jetty lies in Aquinnah, while the east jetty lies in Chilmark. Both towns are in favor of rebuilding the jetties, which were damaged during hurricanes Bob and Sandy. But the towns disagree on the extent of the dredging, which could affect the shellfishing in Menemsha Pond, and would open the pond to larger boats.

Both towns have given permission to the Army Corps to use town-owned areas near the harbor during the jetty project, and Chilmark has also approved the use of the dredge spoils to replenish Menemsha Beach.

But the Chilmark selectmen strongly oppose any dredging south of the red nun, a navigational buoy near the West Basin south of the harbor. In a letter to the Army Corps last spring, they argued that the dredging could harm the shellfish and would encourage larger boats to enter the pond. They cited a review by the Woods Hole Group that said the proposed dredging would have minimal benefits to the pond habitat; and local experts who worried that “a deep, straight channel” would flush out young shellfish before they had a chance to settle.

The jetties and a portion of Menemsha Basin have been federal projects since the 1930s, and the area including Menemsha Pond is a harbor of refuge for ships. But the selectmen disagree with that designation. In the letter, they noted that the pond is used by commercial and recreational boats, but that the largest were only 36 feet: “None could even generously be described as ships.”

The letter mentions that after the most recent dredging of the channel, in 1976, “the pond saw a substantial increase in recreational traffic,” as well as the flushing out of young shellfish.

Commercial fishermen in Menemsha, as well the town shellfish committee and harbor master, are all opposed to dredging south of the red nun, said Chilmark executive secretary Tim Carroll. The addition of larger yachts and sailboats would be a “nightmare” in terms of policing the harbor, and would increase the risk of pollution being dumped or washed overboard, Mr. Carroll said.

Meanwhile, town officials in Aquinnah strongly support the full dredging project, which they say will benefit both shellfishing and the navigation of boats in the harbor area.

“The recommendation that comes from the [Aquinnah] harbor master and shellfish committee is that the channel is definitely in need of dredging,” town administrator Adam Wilson said this week. He added that in addition to the federal project, the town is interested in dredging the West Basin, where it maintains its moorings.

The Wampanoag Tribe of Gay Head (Aquinnah) also supports the dredging.

Buddy Vanderhoop, chairman of the Aquinnah shellfish committee, helped build some of the Island’s jetties and worked for a local dredging company for several years. He recalled that after the dredging in 1976, Aquinnah saw five or six of its best scalloping years ever. “In fact, we went to a 10-bushel limit because they were so big and so plentiful,” he said. “You get more flow, you get more food in there, the scallops can move around a lot easier, and it’s just a great thing to do.”

Aquinnah canceled its commercial scalloping season last year due to a lack of adult scallops on its side of the pond and the discovery of a black algae covering some of the shells. Mr. Vanderhoop said he believes the low flow of water in the pond may have been part of the problem.

The dredging was expected to begin last fall, but project manager Craig Martin said the Army Corps has still not received a water quality permit from the state. As federal projects, the dredging and the jetty rebuilding do not require town approval.

Mr. Carroll the said town officials in Chilmark had been frustrated by the decision of the Army Corps not to hold a public hearing.

The jetty project has taken time to receive funding, but has not yet been delayed. “There is nothing quick about getting federal money for repairs, even for a disaster,” Mr. Carroll said.

Most of the damage to the jetties was seen during Hurricane Bob in 1991, but federal funding became available after Hurricane Sandy in 2012. More recently, during the construction of the Coast Guard boathouse, a portion of one of the jetties was damaged by the water stream from a tugboat that was trying to move a barge. Mr. Carroll said that about 35 feet of the jetty had collapsed under the pressure. “It’s still in place, and according to the contractors that’s going to be a very minor repair,” he said.

The deadlines for rebuilding the jetties are March 31 for the west jetty (to protect piping plovers in the area) and May 21 for the east jetty.