The U.S. Environmental Protection Agency announced a settlement Thursday with Matson Terminals Inc., the company responsible for a 1,400-ton molasses spill in Honolulu Harbor in 2013.

The federal agency said in a statement that Matson will pay a civil penalty of $725,000. The molasses leaked from a section of pipe that had been flagged by the state a year before the spill.

“Dockside facilities must ensure their operations do not pollute nearshore waters,” said Alexis Strauss, EPA’s Acting Regional Administrator for the Pacific Southwest, in the statement. “The Honolulu Harbor spill affected marine life, coral reefs and kept residents and visitors from enjoying the city’s incomparable coastal environment.”

The spill killed more than 26,000 fish and other marine life. Enough molasses to fill about seven rail cars oozed out from a section of pipe Matson thought had been sealed, suffocating marine life and discoloring the water as the sticky substance sank to the bottom of the harbor.

“We are pleased to have reached this agreement with the U.S. EPA,” said Matson CEO Matt Cox in an email to the Associated Press. “Since the spill occurred Matson has worked with all state and federal agencies, and we’ve done our best to make things right. We no longer carry molasses and have decommissioned our pipeline and storage facility.”

The spill shut down much of Honolulu Harbor for nearly two weeks.

The civil settlement follows a criminal case against Matson in which the company paid $1 million in fines and restitution, which was split between the Waikiki Aquarium for coral reef research and Sustainable Coastlines Hawaii for beach cleanups.

The company also reached a settlement with the state to stop transporting molasses through the harbor and paid for cleanup and coral restoration.

Matson is the biggest shipping company connecting Hawaii to the mainland.