“The sediment showed levels of contamination before, but now it’s a hell of a lot worse after this spill,” said Smith.

Water Defense’s analysis showed two things: Metal levels remain elevated in the San Juan’s riverbed, compared with baseline tests, and water in the San Juan was likely contaminated before the Gold King Mine spill.

The EPA declined a request for an interview but stated that it stood by its testing results. The agency also said that it would continue to share data.

“I would say at this point the water is unsafe to use until we have more testing completed,” said Scott Smith, the Chief Technology Officer and Investigator for Water Defense. “We are dealing with known chemicals that are toxic and cancer causing, and we don’t know what’s happening to those chemicals and what’s going on in the crops.”

A new report provided to Al Jazeera by the nonprofit organization Water Defense shows that chromium, lead, beryllium, nickel and nearly a dozen other metals and chemicals have been detected in the river. The results come at a time when other institutions, such as Texas Tech University and New Mexico State University released similar claims .

Now independent testing of the San Juan has concluded that claim may be untrue.

In August, an accident at the defunct Gold King Mine in southern Colorado released nearly 3 million gallons of wastewater that quickly made its way downstream to the Navajo Nation. Earlier this month, the Environmental Protection Agency published testing data from the San Juan River showing that metal concentrations in the water and sediment had returned to pre-spill levels.

For instance, testing showed chromium at 4.7 parts per million (ppm) in sediments affected by the spill. In baseline sediments, chromium was measured at 3.7 ppm. The maximum level set by the EPA for chromium in drinking water is 0.01 ppm.

Investigators found the lead concentration in the San Juan jumped from 7.8 to 9.9 ppm. The EPA says any lead contamination in drinking water is unsafe.

What appeared in sediments after the spill, according to Water Defense, were beryllium and nickel, which have been linked to increased risk of cancer and other health problems.

“The baseline sediment readings are cause for worry even before this spill,” said Smith. “With the impacted sediment, it has just raised this to a whole new level of concern that requires immediate action.”

Upstream, toxic water continues to flow from the Gold King Mine into the Animas River. On Wednesday, the EPA announced that a water treatment system would be deployed to “neutralize the mine discharge and remove solids and metals.”

“This is going to take at least a generation for this cleanup to take place and for the water to be restored,” said Navajo Nation President Russell Begaye. “We need to see some action with removing soil and retesting.”

He said the Navajo land needs to be recognized as a disaster area by the federal government for much-needed funds. He says help from the government would go to removing sediments from the San Juan, building water systems or diverting water from unaffected parts of the San Juan to Navajo farms for the next growing season.

“For [the EPA], the solution is dilution,” said Begaye. “That you add more water to the contaminants and when you add enough, it’ll be safe to drink. It’s impractical.”

In the meantime, irrigation canals to many Navajo farmers are still cut off, and river users are hopeful that when growing season begins next year, the river will be safe to use or an alternative source of water will be available.

“If this were outside of the Navajo Nation and someone reported some kind of toxic plume, this would trigger a whole investigation and fines and basically sequestering off the area,” said Smith. “What applies to the rest of the United States should apply to the Navajo Nation too.”