A federal judge will allow the Trump administration’s Environmental Protection Agency officials to make “substantive changes” to water quality standards for Maine rivers where members of the Penobscot Nation and Houlton Bands of Maliseets have sustenance fishing rights.

The move allows the Trump administration to rework water quality standards the Obama administration set in 2014 in an effort to reduce pollutants, including mercury and dioxins, that make higher-than-average fish consumption unhealthy. The Obama-era standards for the rivers where tribal members have sustenance fishing rights are stricter than those for other water bodies in the state.

The move by U.S. District Judge Jon Levy on Monday is the latest development in a 4-year-old lawsuit between Maine and the federal government. The state sued the EPA in 2014 over what were then proposed water quality standards. The state alleged that, once enacted, the rules would create a double standard for water quality in Maine — one for tribal waters and another for the rest of the state.

In addition to allowing Trump administration officials at the EPA to rework the water quality standards, Levy on Monday ordered that the current Obama-era standards remain in place in the interim. He also allowed attorneys for the Penobscot Nation to file a counterclaim against the state that, if successful, would require Maine “to recognize and protect tribal sustenance fishing rights when setting water quality standards.”

Except for the Penobscots’ counterclaim, Levy stayed the litigation until Dec. 3, 2019.

The tribes opposed allowing the Trump administration’s efforts to revise the standards while the state supported it.

Attorney General and Gov.-elect Janet Mills said Friday that she intends to work with stakeholders to develop new state water quality standards.

“The court’s order sending this back to EPA for reconsideration is an opportunity for us to develop the best water quality standards for Maine waterways, including those which carry special consideration for sustenance fishing,” she said in an email. “When I take office, I intend to work with the tribes, the EPA and all stakeholders to develop new state water quality standards that provide added protections for sustenance fishing in a way that’s consistent with the Settlement Acts. There is no reason why we can’t address this issue and make real progress.”

The impetus for the EPA’s effort to revisit the Obama-era standards was a new Department of Interior opinion issued in April that asserted the Maliseets and other northern tribes in Maine have no federally protected tribal fishing rights; that stated the Penobscot and Passamaquoddy tribes’ rights are limited to sustenance and don’t extend to commercial fishing; and that challenged the Obama administration’s estimate of fish consumption by tribal members, saying it was too broad and “not intended to identify contemporary tribal fish consumption practices.”

Attorneys with the Environmental and Natural Resources Division of the U.S. Department of Justice declined to comment on Levy’s decision because the case still is pending.

Kaighn Smith of Portland, who represents the Penobscot Nation, wrote Thursday in an email that the latest wrinkle in the case would “test Maine’s resolve that the aboriginal sustenance fishing rights of Maine’s tribes carry no right to water quality to ensure that there are safe fish for tribal members to eat.”

“We are pleased that Judge Levy granted the Penobscot Nation’s request to file a counterclaim against Maine,” Smith said. “This tees up the most important issue for resolution: the right of the Penobscot Nation to have water quality to support its reservation sustenance fishery. The Penobscot Nation would hope that the incoming [Gov. Janet] Mills administration and Attorney General [Aaron] Frey would be open to conceding this point, but we are fully ready to litigate the issue.”

A request for comment from the attorney for the Maliseets was not returned.

Historically, Maine’s tribal members have consumed fish and other food sources from the Penobscot, Meduxnekeag and other rivers at much higher rates than the general public, according to court documents.

Maine estimated a fish consumption rate of 1.14 ounces per day for native populations, court documents said. The EPA found that rate was inaccurate and adopted water quality standards to protect the health of tribal members at a consumption rate of 10 ounces of fish per day. That consumption rate most likely will be revised.