BOSTON – A federal appeals court Wednesday rejected a challenge by two Maine Indian tribes to a four-year-old decision that allows the state to regulate the water quality of rivers that run through tribal lands.

A three-judge panel of the 1st U.S. Circuit Court of Appeals concluded that the 1980 settlement of claims by the Penobscot Nation and the Passamaquoddy Tribe to most of the land in Maine gives the state unusual authority that trumps tribal claims of sovereignty.

“…the explicit language of the Settlement Acts establishes state authority that far exceeds what is normal for Indian tribes to which no such legislation applies,” the 25-page decision said.

The dispute over sovereignty has been central to the dispute between the Penobscot and Passamaquoddy tribes and the state over who should have the right to oversee water quality by granting pollution discharge permits on the Penobscot and St. Croix rivers.

The court handed the state a second victory Wednesday by setting aside the EPA’s refusal to allow state jurisdiction over water treatment plants on tribal reservations.

After years of dispute, the Environmental Protection Agency in 2003 decided that the federal government would retain jurisdiction over the treatment plants while the state would control the issuance of permits for the discharge sites.

The tribes had pressed for federal jurisdiction, maintaining that the state Department of Environmental Protection could not be trusted to act in accordance with the interests of fish, wildlife and native people as it grants and enforces the permits.

Over the years, the longstanding dispute over water regulation and sovereignty has generated harsh words, court battles and a number of protests.

In a case that reached the U.S. Supreme Court, tribal leaders were cited for contempt when they refused to comply with a court order to provide paper companies with access to tribal documents related to water regulation.