AUGUSTA, Maine — The U.S. Environmental Protection Agency, which in February directed the state to adopt more stringent water quality standards along the Penobscot River to protect sustenance fishing rights of the Penobscot Nation, has expanded its order to tighten water quality rules across Maine.

The order was delivered to state officials on June 5 by the regional administrator of the EPA, H. Curtis Spalding. In it, Spalding said an agency review of water quality standards has led to its “disapproving on a statewide basis” several rules adopted by the state before May 30, 2000.

This latest ruling by the EPA on Maine’s water quality standards is its third since February. Observers and officials have described these actions as “unprecedented” and say they could have a significant effect on Maine communities and industry.

The regulations disapproved by the EPA include rules that apply to state waivers or modifications of water quality standards, Maine’s criteria for dissolved oxygen in Class A waters and stormwater discharge exceptions in Class AA and Class SA waters.

Class A and AA waters are freshwater rivers, and Class SA waters are defined as marine and estuarine waters, according to the state’s website.

Along with these statewide regulations, the EPA in its decision also disapproved six other regulations specifically for waters in Indian lands, the oversight of which has been the subject of tension and litigation between the state and federal government for years.

In response to the June 5 decision, the Maine Department of Environmental Protection and attorney general responded by filing a notice of an intent to sue the EPA “over [its] recent and related actions … which, among other things, each unlawfully disapprove of Maine’s water quality standards.”

“Many of the standards disapproved by EPA had been in effect protecting Maine’s waters for as much as 30 years,” Tim Feeley, spokesman for the attorney general’s office, said Tuesday.

In a statement issued June 12, the DEP accused the EPA of providing a lengthy document that “does not contain the scientific analyses or information necessary to form the basis of a disapproval,” with information “based on supposition … not based on conclusive data.”

“The Department is considering all legal and administrative options to address the wrongs which EPA has caused,” the DEP statement said. “In the meantime, to provide certainty and predictability for Maine’s regulated community, the department will continue to issue permits based on those standards, as they are fully protective of water quality.”

Feeley said the EPA based its decisions concerning standards for water in tribal lands on a new designated use — tribal sustenance fishing — that “EPA unilaterally created without any public process.”

Then the EPA further indicated that “any different standards ultimately implemented in [tribal] waters will have a broader regulatory reach into non-tribal waters within the same watersheds,” Feeley said.

In addition to the regulatory items that were disapproved, the EPA did approve more than 40 other state regulations in its June 5 letter to Maine Department of Environmental Protection Commissioner Patricia Aho.

Dave Deegan, spokesman for the EPA’s New England Regional Office, said it was “determined that some [standards] could not be approved, either because they did not protect tribal sustenance fishing uses, which are guaranteed by state and federal statutes, or were not consistent with other requirements of the federal Clean Water Act.”

The tribal waters standards disapproved by the EPA included exceptions for naturally occurring toxic substances, pH levels in freshwaters, bacteria regulations for Class AA, A and SA waters and standards for tidal temperatures.

The disapproval of statewide water quality standards were “based on fundamental problems with the water quality standards which would be an issue anywhere,” Deegan said

The EPA rulings come at a time when the Penobscot Nation is suing the state in federal court over the state’s interpretation of whether the tribe’s jurisdictional authority applies to parts of the Penobscot River that abut tribal islands in the river. Originally, 18 municipalities, companies and sewer districts were granted intervenor status in the lawsuit to support the state’s position. In April, Orono withdrew from the lawsuit after community members opposed being involved.

Tribal waters for the Penobscot River start at the Milford Dam — the location of Indian Island — and stretch north about 70 miles to Millinocket.

The Maine DEP states 35 years ago, both Congress and the Maine Legislature established that the Maine Indian Claims Settlement Act and the Maine Implementing Act gave the state primary environmental regulatory authority and jurisdiction throughout the state, including within Indian territories.

The EPA counters the state’s position by saying the federal agency has jurisdiction over the waterways, “because EPA has never acted on pre-2003 [water quality standards] for waters in Indian lands, they remain ‘new or revised’ [water quality standards] as to those waters and thus subject to EPA review and approval or disapproval pursuant to Clean Water Act,” a footnote in the June 5 letter states.

Maine responded in a June 12 letter from Aho and Attorney General Janet Mills that “despite the establishment of Maine’s clear authority, EPA has chosen to ‘take no action’ to approve or disapprove water quality standards for waters in Indian territories for more than 10 years.”

That inaction had prompted the state to sue the EPA in 2014 to force the federal agency to approve the state’s rules for tribal waters, which prompted the federal agency to issue their three far-reaching decisions this year.

Now, the state has until the beginning of August to respond to the EPA rulings, David Madore, spokesman for the Maine DEP, said in an email this week.

Spalding, in his decision, indicated the disapproved water quality standards would remain in effect until the state or EPA come up with new standards.

The Clean Water Act compels the EPA to promptly propose federal water quality standards if the state does not adequately address the disapprovals within 90 days.

Deegan said the EPA “has offered to work with the state and provide whatever support it can, because the agency greatly prefers that Maine take the lead in developing new standards.”