As of November 2020,[update] the mine developer, Northern Dynasty Minerals, still sought federal permits from the United States Coast Guard[2] and the Bureau of Safety and Environmental Enforcement.

Pebble is under a broad flat valley at about 1,000 feet (300 m) above sea level dividing the drainages of Upper Talarik Creek and the Koktuli River.

In the western part of the orebody, mineralization occurs in a complex of several small granodiorite cupolas, diorite sills, older intrusions, breccias, and sediments.

[19][20] Metallic minerals identified at Pebble include pyrite, chalcopyrite, molybdenite, and bornite, along with minor covellite, chalcocite, digenite and magnetite.

There are more than 30 Alaskan native tribes in the region that depend on salmon to support their traditional subsistence ways of life, in addition to other inhabitants and tourists in the area.

[28] In 1987 Cominco Alaska Exploration (CAE) (which subsequently became Teck Resources) collected mineralized surface samples at the Pebble site from color anomalies visible from aircraft.

Three of the world's largest mining companies purchased shares of Northern Dynasty or became partners in the Pebble Limited Partnership through obligations to fund exploration and development.

[54] In April 2017 Northern Dynasty reported that it had received notice of approval of a Miscellaneous Land Use Permit from the Alaska Department of Natural Resources (DNR) for ongoing activities at Pebble.

[69][70] 2010: Nine Bristol Bay Tribes, commercial fishermen, and sportsmen requested the EPA conduct a Section 404c Environmental Assessment study under the Clean Water Act.

EPA describes the study process: "Section 404(c) authorizes EPA to prohibit, restrict, or deny the discharge of dredged or fill material at defined sites in water of the United States (including wetlands) whenever it determines, after notice and opportunity for public hearing, that use of such sites for disposal would have an unacceptable adverse impact on one or more of various resources, including fisheries, wildlife, municipal water supplies, or recreational areas.

"[71] 2012: EPA issued two drafts of the Environmental Assessment, concluding that the proposal for the Pebble Mine would negatively impact the Bristol Bay salmon.

[71] 2015: EPA released its Proposed Determination suggesting to limit mining in the Bristol Bay region due to the irreversible and detrimental impacts it would have on the local salmon ecosystem.

[71] 2016: The Inspector General came out in support of the EPA's Watershed Assessment findings, ultimately encouraging limiting mining due to its unavoidable impact on the salmon wildlife in Bristol Bay, affecting both the natural ecosystem and the economic wellbeing of the area.

[71][74] 2018: Due to increased input of concerns for the Bristol Bay fishery because of Pebble Project, EPA decides to suspend withdrawal of Proposed Determination.

[74] 2020: In July, the U.S. Army Corps of Engineers found in a final environmental analysis that the operation of a Pebble Mine "would not be expected to have a measurable effect on fish numbers" in the Bristol Bay watershed.

[78] 2023: Under the Clean Water Act, the Environmental Protection Agency issued a final determination in January that bans the disposal of mine waste in part of Bristol Bay's watershed.

Some of these assert that even the drilling and other scientific investigations conducted to date have caused significant adverse effects to the land and wildlife near the Pebble site.

[82][83][84] Fifty-seven percent of Alaskan voters in a 2008 statewide election voted against a ballot measure that would have essentially outlawed the project and perhaps similar developments elsewhere in Alaska.

[91] In April 2009, a Native delegation from the Bristol Bay region attended the annual shareholder's meeting of Anglo American, the major mining company behind the Pebble project.

The delegation met with Cynthia Carroll, CEO of Anglo American, claiming that the Bristol Bay watershed is no place for an open-pit mine.

[92] Multiple UK jewelers[93] pledged not to buy gold from the Pebble mine if it is built, joining several American jewelry retailers and manufacturers who had done the same in 2008.

Senator Lisa Murkowski expressed support for the decision but also concern for the precedent it set, and stated that "this must be the only time the EPA ever uses its veto authority under the Clean Water Act in Alaska.

"[114] The Post wrote, "Thiessen described both of the state’s senators, Lisa Murkowski and Dan Sullivan, as politicians who might make noises about the project to appear sensitive to environmental concerns but ultimately won’t stand in their way."

Sullivan also responded saying, "Any suggestion otherwise is either wishful thinking, a blatant mischaracterization, or a desperate attempt to secure funding for a mine that cannot move forward.

In an interview, the executive director of the Environmental Investigation Agency said, "Seeing that the private opinion of that company that their massive plans will be unstoppable once the first artificially sized permit is passed, that is critical information for the public to know before the final decision is made because it clearly may have permanent impacts on an almost priceless resource for Alaska."

This recording and his campaign contributions from the Pebble Mine corporation has led observers to question the sincerity of his opposition to the project, potentially benefiting his political opponent Al Gross.

[118] In April 2013, EPA issued a draft assessment of the impact of proposed mining plans on the fisheries, wildlife and Alaska native tribes in the region.

The suit seeks "Declaratory and Injunctive Relief," asserting that the Alaska Department of Natural Resources repeatedly violated Section VIII of the Alaska Constitution, which specifically provides that there shall be, "...no disposals or leases of state lands...without prior public notice and other safeguards of the public's interest..." The plaintiffs are seeking, among other things, an injunction voiding the project's existing permits, including water-use permits.

The suit also alleges that significant, and documented, adverse effects on land, water, and wildlife have already occurred as a result of drilling and other exploration activities at Pebble since 1989.

[140][141] Then-Governor Sarah Palin was a strong supporter of the project and faced criticism about her opposition to the initiative, the involvement of state government and the intended use of a $7 million federal earmark to facilitate it.