KINGSTON — Boaters going to and from the Port of Kingston may soon find restrictions in Appletree Cove.

In the final permitting stage for its maintenance dredge project, the Port of Kingston’s application has been stopped because of its eelgrass mitigation plan.

“In doing our due diligence, we thought we had everything worked out with the agencies,” said Steve Hyman, the port’s interim director. “But now in this last hour, the mitigation plan we had is not acceptable.”

The problem stems from protection over eelgrass in aquatic lands controlled by the state Department of Natural Resources (DNR). Though the department is not responsible for issuing the dredge permits, it has a say over what work is done. The department is reluctant to allow the port to tamper with eelgrass.

Eelgrass is important in marine and estuarine waters because they are home to small organisms that are food for larger species, such as salmon, which migrate through Appletree Cove. Eelgrass supplies organic material to nearshore areas and its roots stabilize the sediments, according to information from a DNR report.

Without a maintenance dredge, continued silt buildup in Appletree Cove from Carpenter Creek will affect what boats can be launched and when. The boat launch may become a shallow-water launch, Hyman said.

“It will be an inconvenience for some, he said.

A dredge would widen the entrance to Appletree Cove and take away the excess silt that is causing a shallow bottom.

The final permit would be issued by the U.S. Army Corps of Engineers. But the port’s plans were still being reviewed as of Dec. 10, according to corps spokeswoman Patricia Graesser.

“We are close to a decision,” Graesser said. “But we are still working with agencies about eelgrass mitigations.”

Though Graesser was told interested parties are close to a decision, the corps needs a complete review before allowing the port to continue with its project.

The port began applying for permits in September 2012, but has been planning for the dredge since the opening of Carpenter Creek estuary in January 2012. The removal of the too-small fish culvert under West Kingston Road increased sedimentation in the cove, affecting boat traffic. The port declared a state of emergency to speed the permit process when it became clear the cove was becoming shallower because of silt buildup. Boats grounded and A, B and C docks were sometimes inaccessible.

The port has been close to receiving its final permit since November. Hydrographic and environmental surveys were conducted to test the quality of the soil; the soil tested clean and will be disposed of upland. Preliminary estimates put the dredging cost about $450,000.

“We should have got the permit two days before the government [shutdown],” Port Commissioner Pete DeBoer said. However, “something happened in that period” the government was shutdown, he said. “Someone wants to have their signature on it.” Unless the permit is issued in the “next day or two,” DeBoer said the port would have to start the permit process over.

The port’s next window to perform a dredge would be July. Because of salmon migration, work cannot be done from about mid-February to July.

Delaying the project will also affect the bidding process. The port will have to go back to contractors once dredging can begin again.

“It’s been a long haul,” DeBoer said of the project.

If the port does not receive its final permit, it will have to renegotiate the mitigation plan. There are a few options, but Hyman said those options were too early to discuss.