WASHINGTON — One of the nation’s largest coal producers will pay a $27.5 million fine and spend $200 million to reduce illegal toxic discharges into hundreds of waterways across five Appalachian states, according to a proposed settlement Wednesday.
The agreement includes the largest fine ever for violations of water pollution permits. The Associated Press obtained details about the settlement before it was filed Wednesday in federal court in West Virginia.
The discharges occurred in Kentucky, Pennsylvania, Tennessee, Virginia, and West Virginia.
‘‘This is the largest one, period,’’ said Cynthia Giles, head of the Environmental Protection Agency’s enforcement office, told the Associated Press. ‘‘It’s the biggest case for permit violations for numbers of violations and size of the penalty, which reflects the seriousness of violations.’’
The government says that between 2006 and 2013, Alpha Natural Resources Inc. and dozens of subsidiaries violated water pollution limits in state-issued permits more than 6,000 times. They discharged heavy metals and other contaminants harmful to fish and other wildlife from nearly 800 outfall pipes directly into rivers, streams, and tributaries, according to the government.
Monitoring records attached to the complaint show that in some cases, the releases exceeded permit limits by 35 times.
Under the agreement, the mine operators will install wastewater treatment systems and take other measures aimed at reducing discharges from 79 active coal mines and 25 coal processing plants in those five states.
Bristol, Va.-based Alpha, the nation’s third largest coal supplier, estimates those steps will cost about $200 million.
Half the fine will go to the federal government; the other half will be divided among West Virginia, Pennsylvania, and Kentucky.
‘‘Today’s agreement is good news for communities across Appalachia, who have too often been vulnerable to polluters who disregard the law,’’ said Robert G. Dreher, acting assistant attorney general for the Justice Department’s Environment and Natural Resources Division.
The settlement comes nearly two months after the water supply for 300,000 people in and around Charleston, W. Va., was temporarily undrinkable after the spill of a coal-cleaning chemical on the banks of the Elk River.
Last month, a ruptured pipe underneath a coal ash impoundment at a Duke Energy power plant polluted the waters of the Dan River in North Carolina. State environmental officials in that case have cited Duke for not obtaining the proper permits for discharges into waterways.
For the Obama administration, the settlement is likely to generate more criticism from the coal industry, their lobbyists, and supporters in Congress. They have said that this administration is going after coal with new regulations aimed at reducing mercury and other toxic air pollutants from power plant smokestacks, and the first-ever proposal to reduce carbon from yet-to-be-built coal-fired power plants.
But when it comes to water and coal, the administration mostly has played catch-up.
The EPA says coal mining and the burning of coal for electricity are some of the largest sources of water pollution. But the agency has struggled to get a hold on the problem.
Efforts by the EPA to address pollution from mountaintop coal mines have been vacated by a federal court. That decision is under appeal.
There are no federal limits on the vast majority of chemicals that power plants pipe directly into rivers, streams, and reservoirs. The EPA last year proposed setting limits on a few of the compounds, in what would be the first update since 1982.
Before Wednesday’s settlement, Alpha already was hurting. Last year, the company lost $1.1 billion on total revenue of $4.9 billion.
The company acquired Massey Energy in 2011, and more than half of the violations covered by the new settlement stemmed from that company’s operations.