BLUE HILL – The recently issued federal clean water permit for a salmon farm in Blue Hill Bay has raised questions and concerns on both sides of the debate over siting those aquaculture operations.

On Thursday, the U.S. Environmental Protection Agency issued a National Pollution Discharge Elimination System permit for Acadia Aquaculture’s planned salmon farm near Dunham’s Cove off Long Island.

Robert W. Varney, head of the EPA’s New England office in Boston, called the permit the most “stringent, comprehensive and protective” permit ever issued by the EPA, and opponents of the salmon farm sites have questioned whether Acadia Aquaculture’s operation can meet the new requirements established in the NPDES permit.

Opponents of the operation have argued that Acadia Aquaculture will be in violation of the permit as soon as the Dunham’s Cove site becomes operational. Owner Erick Swanson said he doubts whether some of the conditions in the permit will ever be enforceable.

“The Acadia permit from EPA is not usable as it’s written,” he said. “It will have to be modified.”

Swanson said he had discussed these concerns with federal officials during the permitting process and had determined it would be easier to modify a permit after it was issued than to change his application in midstream and go through the public hearing process again.

One key condition in the permit limits the amount of fish feed that can be put into the water at the Dunham’s Cove site and at Swanson’s existing salmon farm located off Hardwood Island, southeast of Long Island in the bay. That limit is set at 2,150,000 pounds per year for the two sites combined.

Limiting the amount of feed effectively limits the number of fish that can be raised at the two sites, according to Don Eley, president of the Friends of Blue Hill Bay, a local group that has fought the state and Swanson over aquaculture siting issues in the bay.

“He’s already got 560,000 [fish] at the Hardwood Island site,” Eley said. “He’s got his permit, but he can’t put any more fish in the water.”

Swanson agreed that condition would limit the number of fish he can put on a site. The Hardwood Island site has slightly under 600,000 fish on it, he said, which required about 1,350 tons of feed during the past year, more than the federal permit will allow. That limit will have to be increased, he said, or he will not be able to use the site.

He also said that the amount of feed used has not had an overall impact on the amount of nutrients in the water or in the amount of plankton growing there.

Swanson said his plan for the operation is to establish four sites in the bay that will allow him to maintain the number of fish he’s now raising and to separate them into two age classes on separate sites, 300,000 fish in each of two age classes. A third site would be kept fallow for a year before restocking, and another would be used to raise brood stock.

Acadia Aquaculture already has applied for two additional leases off Long Island. The Department of Marine Resources has scheduled a public hearing March 13 as part of its review of these applications.

Those leases, however, are for many more fish than are allowed under the federal permit, and more than Swanson is raising now.

If the two pending leases were approved, Swanson would have the combined capacity to raise close to 2 million fish, well above the limit set by the federal permit. The potential for that number of fish in the bay concerns many residents along the Blue Hill peninsula.

That level of activity would jeopardize the water quality in the bay, Eley said.

Another problematic issue in the permit is the requirement that each fish in a pen be marked with a site-specific marker so it could be traced back to a specific pen if it escaped.

The problem with that requirement, Swanson said, is that there is no viable system now that can be used to mark the fish.

“The kinds of markers they’re talking about don’t exist,” he said.

Swanson also said there are legal issues surrounding the marker requirement, and claimed that because the marked fish are handled and moved so many times by different people, it is impossible to determine when during the process a fish may have escaped.

The permit also requires regular monitoring of the ocean bottom under and around the salmon pens as well as the conditions in the waters below the pens. Swanson said the requirements are all things that he has done before on his existing site.

Eley disagreed and said the permit calls for a “significant amount of monitoring that has not been done in the past.”

Despite the questions raised by the permit, Swanson said, he is “happy to have it” and sees it as another step toward establishing a viable operation in Blue Hill Bay. Once he has four sites operating, he said, he will be willing to meet with opponents to discuss other, more acceptable sites, and would be willing to move some pens to accommodate local concerns.

Eley argued that the time for discussing appropriate sites is before the leases are granted and the fish are in the water. That, he said, has been the problem with the state’s approach to the process of granting aquaculture leases in the bay. The crucial issue, he said, is whether there is going to be a plan for the bay.

“That’s our concern. What is going to be the total impact on the bay?” he said. “The state says, ‘Put it in and we’ll find out.’ That’s not good enough. That’s not an effective way to manage public property.”