A federal judge ruled Wednesday that the Penobscot Nation’s reservation ends at the shoreline of tribal islands, siding with the state in a jurisdictional dispute over the waters of the Penobscot River.

But in a mixed ruling, U.S. District Court Judge George Singal reaffirmed tribal members’ sustenance fishing rights throughout the main stem of the Penobscot.

Singal rejected arguments from the Penobscot Nation and federal agencies that the tribe’s reservation boundaries extend “from bank to bank” of Maine’s second-largest river. Instead, Singal sided with Attorney General Janet Mills in ruling there was “no ambiguity” in the definition of the reservation as laid out in the landmark Maine Indian Claims Settlement Act of 1980 negotiated between the state, federal government and tribes.

“The Settlement Acts clearly define the Penobscot Indian Reservation to include the delineated islands of the main stem, but do not suggest that any of the waters of the main stem fall within the Penobscot Indian Reservation,” Singal wrote. “That clear statutory language provides no opportunity to suggest that any of the waters of the main stem are also included within the boundaries of the Penobscot Indian Reservation.”

But Singal rejected the state’s interpretation on the fishing issue and, seeking to clarify what he said was ambiguous language, said the tribe has a “retained right to sustenance fish in the main stem, as it had done historically and continuously.” Under the state’s erroneous interpretation, Singal wrote, tribal members would only be allowed to fish from land.

“There is no evidence that the Maine Legislature, Congress, or the Penobscot Nation intended for the Settlement Acts to change and further restrict the already long-accepted practice of Penobscot Nation members sustenance fishing in the main stem, such that tribal members would need to have at minimum one foot on an island and could no longer sustenance fish from boats in the main stem,” Singal said.

This ruling doesn’t address a dispute over water-quality standards in the waterways that pass through tribal lands. A separate lawsuit on that issue that the state filed against the federal government is pending.

Tribal leaders were evaluating the ruling Wednesday evening and plan to “huddle up” with attorneys from the U.S. Department of Justice, which helped argue the tribe’s case, to discuss next steps, which could include an appeal.

Penobscot Nation Chief Kirk Francis described the ruling as “a mixed bag.” Francis was gratified Singal upheld the tribe’s sustenance fishing rights “from bank to bank” but disappointed that the judge did not believe those waters are part of the reservation. That is concerning, Francis added, because the tribe needs to understand how to manage a resource that members depend on for sustenance.

“Obviously it’s not the greatest decision for the tribe,” Francis said. “We are trying to understand how the existing statute and the decision fit together.”

Mills said the case, which has been watched closely by American Indian organizations around the country, could have had “potentially enormous” ramifications for river users. While the tribe’s attorneys argued that the case was primarily about sustenance fishing rights, lawyers for the state said Penobscots’ interpretation of their boundaries could allow the tribe to exclude fishermen from the river, charge fees for access or even regulate industrial and municipal discharges into the Penobscot.

“The state respects that federal Judge George Singal has digested thousands of pages of filings by all the parties and intervenors,” Mills’ office said in a statement. “In this very thorough 64-page ruling the judge decided very clearly that the reservation itself does not include the main stem of the Penobscot River. The river is, as the state argued, held in trust for the benefit and use of all. The State is equally pleased that the court recognized the historical right of individual tribal members to engage in sustenance fishing along the river, a right which the state has always accorded and never denied.”

The case stems from a 2012 letter from then-Attorney General William Schneider, although the underlying tensions over tribal jurisdiction and fishing rights date back decades.

Responding to reports that tribal game wardens were stopping and summonsing non-tribal sportsmen on the river, Schneider advised the Maine Warden Service and Maine Marine Patrol that the Penobscot reservation does not include the main stem of the river.

“Like private landowners, the Penobscot Nation may also restrict access to their lands, here islands, as it sees fit,” Schneider wrote. “However, the river itself is not part of the Penobscot Nation’s Reservation, and therefore is not subject to its regulatory authority or proprietary control. The Penobscot River is held in trust by the State for all Maine citizens, and State law, including statutes and regulations governing hunting, are fully applicable there.”

The Penobscot Nation filed suit in federal court 12 days later, claiming that any attempt to enforce state law against tribal members who are sustenance fishing in the river “threatens to violate the federal law right of the Nation’s members to be free from state authority over such activity.”

The case is emblematic of the growing rift between Maine’s tribal governments and the LePage administration as well as ongoing tensions over the 35-year-old settlement agreement. In May, the Penobscot Nation and Passamaquoddy Tribe withdrew their representatives to the Maine Legislature and accused the state of attempting to perpetuate a “guardian-to-ward relationship” with the sovereign tribal nations. Mills, meanwhile, is suing the U.S. Environmental Protection Agency over water quality standards in waters that pass through tribal areas.