The Maine Attorney General’s Office has accused the U.S. Environmental Protection Agency of creating an unlawful “double standard” when it comes to water quality and requested that a federal court overturn recent EPA decisions.

The request, filed Friday in U.S. District Court, is part of a broader dispute over water quality standards near Maine’s Indian tribes and the state’s authority under a 35-year-old agreement between the state, tribes and the federal government. The cases could ultimately determine who sets environmental policies on water that flows through tribal lands, with implications for industrial or municipal discharges into rivers, as well as fishing rights and a host of other issues on those rivers and lands.

In February, the EPA disapproved water quality criteria for waters that flow through tribal areas after taking no action on those standards for more than a decade, according to the state. While the state claims the EPA decision violates the 1980 Maine Indian Claims Settlement Acts, federal officials say Maine’s general standards are inadequate to protect tribal members on reservations from some toxins because they eat more fish than the average Mainer.

In the complaint filed Friday, the office of Attorney General Janet Mills argued that the EPA rejected Maine’s water quality standards on unspecified waterways based on a rationale that was “arbitrary, capricious, an abuse of discretion, and/or otherwise not in accordance with the law.” The complaint also asks the court to declare that the EPA has no right to treat “Indian waters” and “non-Indian waters” differently regarding water quality standards or base any decisions on distinctions between Maine’s tribal population and the general population.

“This differential treatment violates both the comprehensive 1980 Maine Indian Claims Settlement Acts and the Clean Water Act,” Mills’ office said in a statement. “Under the Settlement Acts, all Mainers and Maine waters are treated the same for environmental purposes. Maine’s stringent water standards uniformly protect all Maine citizens, including members of Maine’s tribes.”

The state also accused the EPA of engaging in “secret negotiations” with Maine’s tribes for more than a decade through a confidentiality agreement that Mills’ office said violates the Freedom of Information Act.

An EPA spokesman could not be reached for comment Friday afternoon.

Mills’ court filing on Friday was an amendment to a 2014 lawsuit against the EPA seeking to force federal regulators to act on the state’s proposed water quality standards on unspecified tribal waters. The EPA had previously approved the state standards but began distinguishing between tribal and non-tribal waters in 2004. After that point, the agency would approve standards on most waters but would take no action on waters within tribal territories or lands. Instead, the agency said it would “retain responsibility … for those waters.”

That changed again last February, when the EPA ordered Maine to tighten its water quality standards for potential toxins such as mercury and arsenic on waters within tribal lands. But the state claims the EPA took it a step further by claiming there were no water quality standards on those unspecified tribal lands, a fact strongly disputed by Mills’ office in their Friday filing. Further complicating matters, the EPA neither listed which waterways were considered “Indian waters” nor provided standards acceptable to the agency.

Mills’ office said the EPA’s position creates a double standard that violates the terms and intent of both the Maine Indian Claims Settlement Acts and the landmark Clean Water Act legislation, co-authored by the late U.S. Sen. Edmund Muskie, D-Maine, and later reauthorized after a push led by U.S. Sen. George Mitchell, D-Maine.

“EPA has also not answered basic questions about what standards apply in tribal areas, and has even suggested that there are no water quality standards at all for those waters,” Mills office said in a statement. “To the state, this aspect of EPA’s new double standard represents a grave environmental concern. It would shock Mitchell and Muskie, and it should shock all Mainers, to learn that EPA thinks there are no standards in place to protect these waters.”

Next Wednesday, lawyers representing the state and the Penobscot Nation will be in federal court in Portland for a hearing on the other major case that could have more sweeping implications.

In August 2012, the Penobscot Nation sued then-Attorney General William Schneider claiming he was wrongly restricting tribal members’ sustenance fishing rights in the river as well as the rights of the tribe’s game wardens to exercise exclusive authority over hunting, fishing and trapping in the river.

But a key point of contention in the suit was whether the tribe’s rights were restricted to the islands that are part of the Penobscot reservation between Medway and Old Town, or whether that jurisdiction extends to the main stem of the river. Schneider and, subsequently, Mills have argued that the Penobscot Nation can only regulate hunting, fishing and taking of wildlife on the islands. The tribe’s lawsuit contends that Congress, upon ratifying the extent of the reservation, intended that jurisdiction “to encompass ownership rights within and attending the Penobscot River surrounding Indian Island and islands in the river northward thereof.”

The federal government has joined the Penobscot Nation on the case while industries and other groups with interests in the river have sided with the state. A U.S. District Court judge will hear summary arguments in the case on Wednesday before making a decision at a later date.