Chesapeake Energy will pay $3.2 million in fines and spend $6.5 million on restoration work in a settlement over allegations the company buried streams and wetlands without permits at more than two dozen natural gas extraction sites across West Virginia, officials announced Thursday.

The civil settlement covers 27 sites in eight counties and comes just a year after Chesapeake subsidiary Chesapeake Appalachia pleaded guilty to three criminal charges for similar violations of the Clean Water Act’s “dredge-and-fill” permit requirements.

Chesapeake, the nation’s second-largest natural gas producer, also agreed to implement what regulators called a “comprehensive plan” to follow federal and state water-protection laws in the future.

The deal, which is subject to court approval, was announced by the U.S. Department of Justice and the Environmental Protection Agency after first being filed in U.S. District Court in Wheeling.

“With this agreement, Chesapeake is taking important steps to comply with state and federal laws that are essential to protecting the integrity of the nation’s waters, wetlands and streams,” said Robert G. Dreher, acting assistant attorney general for environment and natural resources.

EPA Regional Administrator Shawn Garvin said the case “sends a clear message that [the] EPA and other federal and state regulatory agencies will do what is necessary to ensure compliance with the Clean Water Act and to protect these valuable resources and the health of our communities.”

Gordon Pennoyer, a spokesman for Oklahoma City-based Chesapeake, called the settlement a “key milestone in the settlement process to resolve federal and state claims relating to surface construction activities that occurred in West Virginia prior to November 2010.

“The company is fully committed to regulatory compliance and is working with the Environmental Protection Agency, Army Corps of Engineers and West Virginia Department of Environmental Protection to restore the impacted sites,” Pennoyer said in an email message.