The Environmental Protection Agency said that in 2006-2013, ANR and its subsidiaries violated water pollution limits more than 6000 times.
ANR discharged heavy metals and other contaminants from nearly 800 outfall pipes across five Appalachian states, according to a proposed consent decree by the EPA.
Under the settlement, the mine operators must install wastewater treatment systems and take other measures to reduce discharges from 79 active coal mines and 25 coal processing plants.
In a statement, acting assistant attorney general Robert Dreher said: “The unprecedented size of the civil penalty in this settlement sends a strong deterrent message to others in this industry, that such egregious violations of the nation's Clean Water Act will not be tolerated”.
The EPA accused ANR of routinely violating water pollution limits and, on occasion, discharging pollutants into waterways without a permit.
The pollutants included iron, pH, total suspended solids, aluminium, manganese and selenium.
The federal government will share the $27.5 million settlement money with three states. West Virginia will receive $8.9 million, Pennsylvania will get $4.1 million, and Kentucky will get $687,500.
Alpha senior vice-president of environmental affairs, Gene Kitts said in a statement, “For an organisation our size and with as varied a group of mining operations and permit conditions as we have, our people do an outstanding job in maintaining environmental compliance,
This settlement will provide a consistent structure to our efforts to become even better in preventing incidents and in responding quickly to situations where permit limits are exceeded.”