Patriot Coal Corp. was found in contempt of court by a federal judge on Wednesday and ordered to clean up selenium pollution at two mines in West Virginia.

U.S. District Judge Robert Chambers ordered Patriot subsidiary Apogee Coal to install treatment systems and comply with discharge limits by March 1, 2013.

Patriot subsidiary Hobet Mining was ordered to submit a selenium treatment plan by Oct. 1 and comply with pollution limits in its operating permit by May 1, 2013, Patriot said in a statement.

The Creve Coeur-based coal producer estimates the it will cost $50 million to comply with the judgment, plus $3 million in annual operating costs. Chambers also ordered Patriot to post a $45 million letter of credit to guarantee the treatment systems are installed.