"The agency worked hard to find a way in which it could pay individuals for damages due to the incident, but unfortunately, our hands are tied," EPA spokeswoman Nancy Grantham said.
The EPA said it has spent more than $31.3 million on the spill, including remediation work, water testing and payments to state, local and tribal agencies.
A total of 73 claims were filed, some by farmers who lost crops or had to haul water because rivers polluted by the spill were temporarily unusable for irrigation and livestock. Rafting companies and their employees sought lost income and wages because they couldn't take visitors on river trips. Some homeowners sought damages because they said their wells were affected.
"We had direct revenue losses of $50,000-plus," said Alex Mickel, owner of Mild to Wild Rafting in Durango, Colorado.
Mickel said the EPA had left him with the impression it would compensate for economic losses.
"That just amazes me that they would do just a complete reversal," he said in an interview. Mickel said he would consult with his attorney on his next move.
The August 2015 spill at the Gold King Mine in southwestern Colorado released 3 million gallons of wastewater tainted with iron, aluminum, manganese, lead, copper and other metals. The Animas and San Juan rivers in Colorado, New Mexico and Utah were polluted, with stretches of waterway turning an eerie orange-yellow.
Some of the affected rivers pass through Indian reservations.
Navajo Nation President Russell Begaye said the nation would keep pushing for compensation.
"It was devastating to both the Navajo Nation and to the farmers," he said. "Even today, people still question if the water is clean enough for farming, livestock or human consumption."
The EPA has said water quality in the rivers has returned to pre-spill conditions.
Members of Congress expressed anger and disappointment at the EPA decision. New Mexico Sens. Tom Udall and Martin Heinrich and Rep. Ben Ray Lujan, all Democrats, accused the agency of reneging on a pledge.
"We are outraged at this last-ditch move by the federal government's lawyers to go back on the EPA's promise to the people of the state of New Mexico and especially the Navajo Nation that it would fully address this environmental disaster that still plagues the people of the Four Corners region."
Members of Colorado's congressional delegation said they would introduce legislation to repay economic damage.
"When the law allows the government to hide from those whom it has harmed, the law must change," Colorado Republican Sen. Cory Gardner said.
An EPA-led contractor crew triggered the spill while doing exploratory excavation work at the mine entrance in advance of a possible cleanup. The Gold King is one of hundreds of inactive mines in the Colorado mountains that continuously spew polluted water into rivers or have the potential to do so.
The EPA has designated the area a Superfund site to pay for a broad cleanup. Initial research is underway.
State, federal and tribal officials have been harshly critical of the EPA for causing the spill and for its handling of the aftermath, including the costs. The Navajo Nation and the state of New Mexico have already sued the agency in federal court, and other lawsuits are likely after Friday's announcement.
Last month, the EPA said it would pay $4.5 million to state, local and tribal governments to cover the cost of their emergency response to the spill, but the agency rejected $20.4 million in other requests for past and future expenses, again citing federal law.