A winter-long dredging project in the Aquinnah Herring Creek is on pause after a crew hired by the Wampanoag tribe came up short on a government-mandated deadline for completing the project.

Bret Stearns, natural resources director for the tribe, said the project is about halfway complete but needs to halt now due to federal regulations that prohibit dredging during the winter flounder spawning season.

Spanning Menemsha and Squibnocket ponds, the historic herring run is an essential part of the annual migration for river herring, which spawn in Squibnocket Pond. The creek had been slowly filing with silt and sand for years, exacerbated by severe storms that have degraded the banks, Mr. Stearns said.

The $250,000 project was authorized as part of a $670,000 federal coastal resiliency grant awarded to the tribe in 2014, after Hurricane Sandy damaged more than 230 acres of coastal ponds and beachfront in Aquinnah. A stringent federal permitting process delayed the project for years. Mr. Stearns said the dredging permit is valid until the project is completed, and work will resume when the last herring have left their spawning grounds in Squibnocket Pond, likely in July.

The work is being carried out by a crew of three employed by Marine Network LLC. Mr. Stearns said the crew ran into more obstacles than expected, including bog material and sticks that clogged the dredging pipe along with more silting than anticipated.

“There was a huge spit that was very difficult to navigate around,” he said. “You could stand in the middle of the stream in sandals and not get your feet wet.”

The project was successful in carving a deeper channel on the Squibnocket side of the creek, transforming two narrow streams that were six inches deep to one 13-foot wide stream that is now two and a half feet deep. The Menemsha Pond side of the creek already had flow over a foot deep, enough for herring to safely pass through.

“We had hoped to advance a little further in the dredging than we did, but we took out the largest impediment, and this year’s [herring] run will be greatly enhanced because of that,” Mr. Stearns said. “There is going to be free and safe passage this year. That’s a win.”

He also said the project is on budget.

Mr. Stearns estimated a total of 400 cubic yards of sand has been dredged to date, with an estimated 800 cubic yards still to go.

Until then, Mr. Stearns said he and his crew will be working to armor the creek banks using vegetation and other soft methods of restoration. They will also replace a single culvert with a double culvert, which will strengthen the flow of the current. A wooden platform that crosses the creek will be rebuilt.

In addition to hitting the mandatory federal deadline for winter flounder spawning, Mr. Stearns said it was important to move the dredging equipment before the first herring begin their annual spawning migration through the creek, likely sometime later this month.

“In terms of getting the real goal done, which is safe passage for the herring, this was a success,” he said, adding that he hopes to see the results on the tribe’s underwater camera, which monitors fish moving between the two ponds.