A shipping line that spilled 12,500 gallons of oil into the Cooper River and Charleston Harbor a decade ago will pay damages to federal and South Carolina departments and could begin restoring damaged marshlands in the coming months, according to new federal court filings.

Evergreen International S.A. will pay $121,000 to the U.S. Department of the Interior to compensate for lost recreational use of natural resources due to the spill, according to the consent decree filed Tuesday in U.S. District Court in Charleston. The damages will go to a special fund for restoring damaged natural resources.

Additionally, Evergreen will reimburse more than $792,000 to the Interior Department and to the National Oceanic and Atmospheric Administration for the costs to those agencies of assessing the damage that affected about 30 linear miles from the former Navy base to Folly Beach.

The S.C. Department of Health and Environmental Control will receive about $1,500, and the S.C. Department of Natural Resources will receive about $27,000 for costs incurred to assess the spill’s damage.

The damages outlined in the filings come on top of about $4 million Evergreen already has paid for the cleanup effort, which involved bird rescues, boat and pier cleaning and reimbursement for property damage.

“Anytime we can attain positive restoration efforts from an oil spill it is good news,” said Mark Musaus, Deputy Regional Director for the U.S. Fish and Wildlife Service. The service is a bureau of the Interior Department. “The funds from this settlement for restoration will result in a better environment for us all,” he said in the statement.

In 2002, Evergreen’s ship struck a submerged steel dredge pipe and polluted shores and marshes along Noisette Creek at the former Navy base. A shellfish bed was closed and recreational shrimp baiting in the area was disrupted. Wildlife, boats and piers were harmed.

The decree outlines the plan to restore and enhance nearly 12 acres of marshes. Restoration will begin following a 30-day public comment period.

Evergreen spokeswoman Barbara Yeninas said Wednesday the cleanup plan was determined “a long time ago.”

In a statement released Thursday, Evergreen called the filing “a routine step in the process of resolving claims for natural resource damages.”

The company “has fully cooperated with the relevant governmental agencies throughout the lengthy (natural resource damages) Assessment process that has led to a settlement agreement...” the Taiwan-based company said in the statement.

Sean Houseal, a local attorney representing Evergreen, did not return a message seeking comment.

Ross Nelson, president of Tidewater Environmental Services, a Johns Island company serving as a consultant on the project, also did not return a message seeking comment.

Reach Renee Dudley at 937-5550 or on Twitter @renee_dudley.