The blow to the tribes' sovereignty came one day before August 9, the annual International Day of the World's Indigenous People, marked at United Nations Headquarters in New York and at ceremonies around the world.
The Penobscot Nation and the Passamaquoddy Tribe had sought to set their own standards under the Clean Water Act. But the 1st Circuit Court of Appeals said the Maine tribes lost those powers when they settled their land claims.
Under special acts of Congress, the state's 'authority far exceeds what is normal for Indian tribes to which no such legislation applies,' Judge Michael Boudin wrote in the unanimous decision.
'This markedly contrasts with the status of Indian tribes in other states not subject to the settlements acts,' the judge wrote.
The decision comes in a long-running battle between the tribes, the state and the Environmental Protection Agency. No one fully agreed on the extent of the tribe's rights versus the state's and the matter festered under the Clinton and Bush administrations, according to Indianz.com, a native American media organization that has covered the case.
The Clean Water Act empowers the EPA to issue permits for the discharge of pollutants into navigable waters. The law entitles states to administer their own permitting programs in place of the EPA's, but to do so a state must apply to the EPA. If the state has 'adequate authority to carry out the described program,' and other requirements are met, the EPA 'shall approve' the program.
In a permitting plan submitted to the EPA, the state of Maine asserted jurisdiction over Penobscot and Passamaquoddy lands.
The tribes claimed that their sovereignty took precedence over state jurisdiction.
The EPA approved the state's plan to regulate water at 19 off-reservation sites, even though some of the sites discharge water into the Penobscot and Passamaquoddy reservations. The court ruling backed this arrangement.
But the agency blocked the state from regulating discharges at two sites owned by the tribes and reserved the right to object to future state actions that might affect tribal subsistence.
The court rejected the tribes' broad reading of their two 1980 settlement acts, citing Maine's 'explicit authority over tribal lands and natural resources' under the laws.
'Maine's power over the southern tribes greatly narrows ordinary tribal sovereignty vis-a-vis state law,' wrote Judge Boudin.
The court ruled that the EPA was in error about the two tribal-owned sites. Regulating water quality is not an 'internal tribal matter' as that term is contemplated by the Maine settlement acts, the judge wrote.
'Discharging pollutants into navigable waters is not of the same character as tribal elections, tribal membership or other exemplars that relate to the structure of Indian government or the distribution of tribal property,' he wrote.
Finally, the court said it was too early to rule on the EPA's claim that it has a general environmental trust responsibility to the tribes to protect their subsistence rights. Both tribes depend on water in the Penobscot and St. Croix rivers that will be regulated by the state of Maine.