Patriot Coal Corp. (PCX) will pay a $6.5 million fine to settle violations of the Clean Water Act, the third-largest for discharge permit violations.

The company has also agreed to what the federal government and West Virginia called "extensive measures" to ensure it complies with the Clean Water Act at mines in the state. Steps include starting a company-wide compliance system and conducting regular internal and third-party audits.

Patriot Coal will also perform five stream-restoration projects in local waters.

The state and federal governments had filed a joint complaint alleging Patriot violated its Clean Water Act permits more than 1,400 times from 2003 through 2007. They said Patriot allegedly discharged excess amounts of metals, sediment and pollutants into rivers and streams in West Virginia.

Last month, Patriot said it was idling four mines in Central Appalachia and cutting 400 jobs amid softening demand. It had already shuttered one mine earlier last month because of high costs and weak market conditions.

Patriot's shares were recently up 2.5% at $4.86. The stock has lost two-thirds of its value in the last three months.

-By Kerry E. Grace, Dow Jones Newswires; 201-938-5089; kerry.grace@dowjones.com