PLEASANT POINT, Maine — To 21st century sport fishermen alewives are a freshwater pest, saltwater trespassers who compete for habitat with prized freshwater bass.

To Passamaquoddy tribal members, whose settlements on both sides of the St. Croix River separating Maine and New Brunswick date back 4,000 years, the prolific fish are seen as an important food source and as a critical element in the diverse marine ecology of Passamaquoddy Bay.

A two-day, 100-mile “sacred run” was held over the weekend between the Pleasant Point settlement and an ancient tribal fishing site at Mud Lake Stream near the New Brunswick community of Forest City. The run was organized by a group called Schoodic Riverkeepers, which is made up of tribal members from both sides of the U.S.-Canadian border who are focusing on restoring their ancestral river and the indigenous populations of marine species in the St. Croix River.

“These fish populations, especially siqonomeqok [alewives], are especially important to the Passamaquoddy and are essential to the health of our ancestral marine waters,” said Vera Francis, one of the event’s organizers.

For 17 years, the annual freshwater migration of countless tens of thousands of saltwater alewives has been blocked by a barrier on the St. Croix River at the Grand Falls Dam fishway that keeps the fish from swimming farther upstream to spawn. The Passamaquoddy want that barrier removed.

In a letter sent May 24, 2012, to the International Joint Commission that works to resolve disputes involving the waters separating the U.S. and Canada, Clayton Cleeves, Passamaquoddy tribal chief of the Pleasant Point Reservation, said his people want to see all alewife barriers removed.

“I urge you to consider the free passage of alewives to their breeding grounds along the St. Croix watershed and into the northern lakes in the state of Maine,” Cleeves’ letter reads in part. “This special request will eliminate all barriers and blockades and will give alewives the freedom to breed at proportions bestowed by the Great Spirit.”

Cleaves said Saturday there are three major barricades that, in effect, shuts off 98 percent of alewives’ natural spawning habitat. “They can’t get up to their maternity ward,” he said.

Cleaves was joined early Saturday morning at the start of the relay run by Hugh Akagi, the chief of Passamaquoddy people who live on the Canadian side of the St. Croix River. He remembers as a 10-year-old boy walking with his father on the beach and seeing six-foot salmon that had washed ashore. Decades later, that scenario has been replaced by pens of farmed salmon sequestered in underwater pens located in waters in and around Passamaquoddy and Cobscook bays.

“What’s happened to the alewives is a reflection of what’s happened to ourselves, in terms of an indigent species being displaced from our natural territory,” Akagi said Saturday. “Everything contributes to balance in nature. Getting back to it is healthy, but we’re watching it spiral in the right direction.

“This was one of the most incredible bays in the world,” said Akagi, a scientist who spent 33 years teaching and later working at the Marine Resource Center in St. Andrews, N.B. where he studied the effect on the tribal waters of aquaculture and the introduction of pollutants. “That’s why the whales and porpoises come, and we used to have a bay full of salmon, haddock, halibut and pollock. How do you restore that? Certainly not by getting rid of what they eat. I’ve seen a lot of habitat desecration.”

A week after Cleaves’ letter to the International Joint Commission, the Portland-based Conservation Law Foundation filed a lawsuit against the federal Environmental Protection Agency that calls for restoration of alewife passage in the St. Croix River.

The suit alleges that the EPA failed to review changes to a Maine law that blocks passage to 98 percent of alewives’ natural, available habitat on the St. Croix as they are required to do under the Clean Water Act. The suit further alleges that as a result of this unsubstantiated obstruction, the Maine Legislature has intentionally and effectively changed the fundamental water quality standards of the St. Croix River, and that the EPA failed to fulfill its legal obligations to review and reject that change.

“For far too long Maine law has prevented alewives, a critical forage fish for birds, fish and mammals, as well as a key source of bait for the Down East lobster industry, from returning to their native waters,” said Sean Mahoney, a vice president and director of CLF Maine. “This law was based on anecdotal information in 1995 that has since been proven entirely wrong by state and federal scientific and peer-reviewed studies. The law is fundamentally at odds with the legal requirement that the St. Croix River provide natural habitat unaffected by human activity for these fish and EPA has a continuing obligation to review and reject this change in that requirement.”

The first day of the Passamaquoddy relay was scheduled to take runners from the Pleasant Point settlement to the Grand Falls Dam fishway on Saturday. Those running on Sunday planned to cover the distance between Princeton and Forest City, N.B.