SEATTLE — BNSF Railway Co. agreed to pay $1.5 million for Puget Sound restoration projects to resolve a lawsuit over storm water pollution at its Seattle facility.

The Puget Soundkeeper Alliance sued BNSF in 2009, alleging it violated federal clean-water laws with storm water discharges from its Balmer Yard facility.

Last August, U.S. District Court Judge John Coughenour found BNSF responsible for numerous federal clean-water violations at the facility.

Under a consent decree filed in federal court this week, BNSF will pay the $1.5 million to a third-party group for projects to improve water quality in Puget Sound. The U.S. Justice Department and Environmental Protection Agency, however, have 45 days to review the consent decree before it becomes legal.

"It sends a strong message that storm water pollution is an important issue and has serious consequences for polluters," said Chris Wilke, executive director of the alliance. "These pollutant levels were particularly concerning because a facility as large as the Balmer Yard can discharge a significant amount of industrial storm water into Puget Sound."

Industrial storm water can contain petroleum and levels of heavy metals that can be harmful to fish and other aquatic life.

The settlement is one of the largest involving citizen actions taken under the federal Clean Water Act involving storm water pollution, Wilke said.

The consent decree notes that BNSF has taken major steps to control storm water pollution from the Balmer Yard facility, including developing a prevention plan, coating roofs to minimize zinc pollution, covering trash bins and minimizing soil erosion.

A call to a BNSF spokesman Gus Melonas on Friday was not immediately returned.

BNSF will pay the $1.5 million to the California-based Rose Foundation for Communities and the Environment, which will then award local grants to improve the water quality of Puget Sound.

"It is a large amount of money and we want to make sure that the projects proposed are well designed," Wilke said.