EPA ruling could strengthen protections for endangered fish in San Juan River

Posted by Donovan Quintero | Apr 3, 2026 | News |

WINDOW ROCK

The endangered Colorado pikeminnow and razorback sucker could gain stronger protections after a federal appeals court ruled that the Environmental Protection Agency failed to fully review how its cadmium guidance could affect threatened wildlife.

The ruling could reach far beyond one toxic metal. It could reshape how water quality standards are updated, how endangered fish are protected in the San Juan River and how large industrial facilities, including the Four Corners Power Plant, are reviewed on and near Navajo land.

The 9th U.S. Circuit Court of Appeals ruled March 3 that the EPA had to consult federal wildlife agencies before issuing its 2016 cadmium water quality guidance. The court found that even though the EPA described the guidance as nonbinding, it still carried real force because states and federally recognized tribes often rely on it when setting or updating water quality standards.

At the center of the case was a challenge by the Center for Biological Diversity, which argued EPA should not have issued the 2016 guidance without first examining how it could affect threatened and endangered species. The court agreed.

The opinion found that cadmium, a toxic metal linked to mining, industrial wastewater and agricultural runoff, can harm aquatic life even at low levels. It also found that the EPA’s 2016 update weakened one key freshwater standard for long-term exposure, making it less protective than the 2001 version.

The court sent the matter back to the EPA and ordered the agency to consult federal wildlife officials before moving forward.

For the Navajo Nation, the ruling matters because the tribe already works within the same federal system states use to set water quality rules. The EPA has approved the tribe to administer water quality standards for its waters, and the Navajo Nation EPA operates under its own Clean Water Act, surface water quality standards and water quality certification regulations.

Most directly, the ruling could shape future updates to tribal water quality rules. The ruling states that when the EPA issues new water quality guidance for pollutants, states and federally recognized tribes must consider that guidance during their next review of water standards. The Navajo Nation would not be required to adopt every EPA recommendation word for word. But if the EPA strengthens its pollution guidance after wildlife review, the new standard could influence how Navajo regulators revise tribal rules in the years ahead.

The decision could also affect the San Juan River system, home to two federally endangered native fish, the Colorado pikeminnow and the razorback sucker. Federal wildlife officials say recovery work in the basin is meant to protect those species while allowing continued water development under tribal, state and federal law.

In the Navajo context, that concern reaches a river system already burdened by irrigation, energy development, wastewater discharges and long-running conflicts over water use.

The Navajo Nation also has authority to review whether certain federally permitted projects would meet tribal water quality standards. If the EPA issues stronger pollution guidance after consulting wildlife agencies, that could raise the benchmark used in future project reviews involving tribal waters.

The effects may also reach the Navajo Agricultural Products Industry, the tribe’s large farm operation in the San Juan River system. The ruling does not create a new permit requirement for NAPI. Still, because NAPI operates in a watershed governed by both tribal and federal water quality rules, tougher future guidance could raise expectations for the waters the farm uses, drains into or affects.

EPA permit materials show the Four Corners Power Plant has wastewater streams that include metal-cleaning wastes, sanitary wastewater and ash pond-related flows regulated through the federal permitting system on Navajo land. That makes Four Corners the kind of facility that could be affected by stricter pollution guidance if the EPA revises cadmium or similar pollutant benchmarks after wildlife review.

Over time, stronger federal guidance could influence permit limits, discharge reviews and oversight standards for facilities whose wastewater reaches protected waters or tributaries. The same logic could extend to nearby cities, towns and other large industrial operations if they discharge wastewater or need permits tied to water quality limits.

While the ruling does not directly change Navajo law or immediately impose new restrictions on NAPI, the Four Corners Power Plant or nearby communities, it does make it harder for the EPA to issue future pollution guidance without first accounting for endangered species and the waters they depend on.

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