The deal announced Tuesday is between St. Louis-based Arch, the Environmental Protection Agency and the Department of Justice.
Arch will take steps to prevent 2 million pounds of pollutants from entering waterways each year. It will also use a treatment system to reduce the amount of selenium pollution.
Senior vice president Paul Lang says Arch is committed to being responsible a steward of the environment.
He says Arch had a 99 percent compliance rate between 2003 and 2010, but the company regrets past violations and is taking aggressive steps to see they aren't repeated.