MINNEAPOLIS — The federal Environmental Protection Agency has reversed itself and rejected a variance that let the Mesabi Nugget iron processing plant near Hoyt Lakes violate Minnesota water quality standards.

Environmental groups and Chippewa bands filed a lawsuit last year challenging the EPA’s 2012 decision to grant the variance, saying it improperly allowed the plant to exceed state standards for discharges of bicarbonates, conductivity, hardness and total dissolved solids. They said the discharges threaten wild rice and other aquatic organisms downstream.

In papers filed in federal court on Wednesday, the EPA said its regional director, Susan Hedman, signed a letter disapproving the variance. One document said the state did not fully justify the nine-year period of the variance and did not provide sufficient evidence that Mesabi Nugget can’t comply sooner than 2021. While the EPA had agreed in March to reverse the variance, the filings made it official.

Paula Maccabee, an attorney for the environmental group WaterLegacy, said Thursday that the significance of the EPA’s decision is that if a company or the state says it’s not feasible to comply with water quality standards, “they can’t just say it, they have to provide the evidence.”

Hedman’s letter said that if Mesabi Nugget and the Minnesota Pollution Control Agency choose to pursue a variance that’s revised to comply with federal requirements, it needs to provide sufficient notice and a chance for the public to comment before resubmitting it to the EPA.