The court said it would not reconsider a 2013 appeals court decision that found the EPA had authority to remove Clean Water Act permits after they were already granted by the US Army Corps of Engineers.
The dispute is over the Spruce No. 1 mine in central Appalachia, which received a permit from the Corps in 2007 to release material at nearby waterways.
The EPA began efforts to modify or suspend the permit in 2009, claiming new information showed that dumping mining waste would impose undesirable harm on water quality and wildlife in the area.
The EPA's actions were completed in 2011 and had since barred Arch Coal's Mingo Logan subsidiary from discharging material into two of the streams that were previously approved disposal areas.
In a petition to the Supreme Court, Mingo Logan said the EPA's move would limit activities at the mine by 88%.
The company claimed it had spent many years and millions of dollars to acquire the original permit.
In its petition it argued that overriding the original permit would create uncertainty in industries that invested billions of dollars in the confidence of permits issued by the Corps.
The EPA had urged the Supreme Court to withdraw from the case, saying the language of the Clean Water Act was clear in giving the agency the power to remove permit terms even after a permit was issued.