WASHINGTON — The Obama administration is proposing a record fine for thousands of water pollution violations by coal mine operators in five Appalachian states.

Alpha Natural Resources, the nation’s third-largest coal supplier, will pay a $27.5 million fine and spend $200 million to reduce illegal toxic discharges from 79 mines and 25 coal processing facilities in West Virginia, Tennessee, Pennsylvania, Virginia and Kentucky.

The deal, which marks the largest fine ever for violations of water pollution limits, was filed in federal court Wednesday. It comes after a series of coal-related spills in West Virginia and North Carolina have raised questions about whether state and federal environmental officials are doing enough to curb water pollution from companies mining, processing, transporting and burning coal.

Advocacy groups said that environmental officials should do more to prevent pollution from entering waterways.

Officials with the Environmental Protection Agency and Justice Department characterized the deal as historic and said the fine was large enough to deter others in the coal industry from flouting the law.

But advocacy groups said state and federal authorities needed to do more to prevent the pollution from occurring in the first place. Environmental groups have filed lawsuits in several states to enforce the law in situations where they have felt the state and federal government have fallen short. In West Virginia, lawmakers and the governor have tried to thwart those efforts with legislation.

The government says that between 2006 and 2013, Alpha Natural Resources 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. There is no evidence that any of the violations contaminated drinking water, EPA officials said.

Monitoring records attached to the complaint show that in some cases, the releases exceeded permit limits by as much as 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 estimates those steps will cost about $200 million.