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West Virginia-based independent Trans Energy was ordered Tuesday to pay a $3 million civil penalty and restore damaged areas for Clean Water Act violations that included illegally filling wetlands and damaging streams in West Virginia.

The Department of Justice (DOJ), the U.S. Environmental Protection Agency (EPA) and the West Virginia Department of Environmental Protection (WVDEP) claimed that 15 sites in West Virginia were damaged by unauthorized discharges of dredge and fill material.

The federal government and WVDEP said the unauthorized discharges were made in order to construct well pads, impoundments, road crossings and other facilities related to natural gas extraction.

The regulators alleged that the violations impacted 13,000 linear feet of stream and more than an acre of wetlands.

The penalty money will be divided equally between the federal government and WVDEP.

The violations were flagged by the EPA in 2011 and 2012 after they were discovered by the WVDEP during routine field inspections.

In 2014, Trans Energy conducted an internal audit and disclosed alleged violations at eight additional locations.

All alleged violations are being resolved with the settlement.

The Clean Water Act requires a company to obtain a permit from the EPA and the U.S. Army Corps of Engineers before discharging dredge or fill material into wetlands, rivers, streams and other waters of the United States.

The settlement is subject to a 30 day public comment period and court approval.