Federal officials are proposing scaled-down regulations to close a loophole they say is threatening more than 300 square miles of federally protected coastal waters in the Gulf of the Farallones National Marine Sanctuary with the introduction of non-native and genetically modified species.

The proposed restrictions, which were endorsed by the Gulf of the Farallones’ advisory council on Wednesday, have been pared back from an 2008 proposal that would have put a cap on Tomales Bay mariculture.

The current proposal would allow current and future mariculture with introduced species like oysters, mussels and clams in all 10.3 square miles of Tomales Bay—as well as catch-and-release of the non-native striped bass throughout the sanctuary and in another protected area off of the coast of Monterey. 

Staff of the National Oceanic and Atmospheric Administration and members of the advisory council have said that aquaculture operations—a nearly $4 million annual harvest in Tomales Bay—are at odds with the agency’s mission to protect and preserve natural habitats. Those statements were included in its online description of the challenges facing estuaries and in a public letter by the leaders of the Gulf of the Farallones advisory body.

Introducing non-native species and genetically modified species is already prohibited in all non-state waters—about 978 square miles—that fall within the sanctuary.

John Finger, co-founder of the Marshall-based Hog Island Oyster Company, said he has asked the government to “slow down on their regulations” because they lack a solid environmental basis and were not subject to sufficient public scrutiny.

‘They really didn’t consult with industry; they didn’t consult with the state. They kind of moved ahead because they were having some heartaches about how they were looking at it themselves,” Mr. Finger said. “We’re already growing introduced species here. [Even] by doubling the amount [of shellfish] you’re not increasing the amount of anything invasive.”

He added: “The only place you can do introduced species in the sanctuaries right now is in Tomales Bay. And while that may be the only place where we’re currently growing introduced species, I don’t know if that’s the only place we’ll ever grow introduced species… Why take that off the table before we’ve even gotten started?”

Gulf of Farallones Superintendent Maria Brown said their proposed rule came in response to solicited public feedback that favored banning new introduced species. She said the protections would include requiring state officials to consult with the federal government before expanding mariculture in Tomales Bay to ensure that “if there’s any expansion, it’s done with as minimal possible impact possible.”

The federal government’s initial proposal was rejected in 2008 by then-Governor Arnold Schwarzenegger, who wanted an exemption that would allow all state-permitted aquaculture on state lands and waters within the sanctuary, which was created in 1981. The California Coastal Commission opposed the governor’s conditions, federal officials said.

The California State Lands Commission and the office of Governor Jerry Brown did not respond to a request for comment, but federal officials said they developed the policy in close consultation with state officials to prevent the policy from being challenged. 

A 2008 study by the Department of Fish and Wildlife found that about 15 percent of the aquatic organisms found in Tomales Bay, or 46, were introduced. Another 47 organisms were of undetermined origin. The most vexing introduced species in the bay include invasive species like the European green crab, which feeds on native clams and oysters and competes with them for resources, and a gelatinous tunicate that suffocates shellfish. In many cases the species are believed to have been introduced by ballast water discharged by ships. 

A mooring plan for Tomales Bay is currently before federal authorities includes educational outreach to show boaters how to prevent their vessels from spreading invasive species.

George Clyde, who sits on the advisory council, said the proposed regulations would not likely impact boating in Tomales Bay because moored vessels do not pick up invasives, launched boats and visiting yachts would not be likely to bring new invasives and no cargo boats enter the bay.

Meanwhile Tomales Bay shellfish growers say they are highly regulated and only cultivate seed that does not import exotic invasive species.