Seven environmental groups sued BNSF last summer, alleging it violated federal law by allowing coal dust, coal chunks and other pollutants to spill into protected waterways from open-top railcars.
U.S. District Court Judge John Coughenour denied BNSF's motion to dismiss the case. The railroad company argued the groups didn't give sufficient notice and didn't have proper standing to sue.
Trains currently carry coal from the Rockies through Spokane, Seattle and along the Columbia River Gorge to an export terminal in British Columbia. More such trains are expected if proposed coal-export terminals are built.
Two projects in Washington - at Cherry Point north of Bellingham and Longview - and one near Boardman, Ore., could bring millions of tons of coal by train through the state for export to Asia. The proposals are undergoing environmental reviews.
The environmental groups, including the Sierra Club, Puget Soundkeeper Alliance and RE Sources For Sustainable Communities, say coal and coal dust fall off the railcars through holes in the railcars or when coal trains pass through rough tracks or are blown off during high winds or fast speeds.
They argue that BNSF violated the federal Clean Water Act by discharging coal into local rivers without a permit.
The same groups filed a nearly identical lawsuit against BNSF in federal court in Yakima. In January, Judge Lonny Suko also denied the railroad company's motion to dismiss that suit. That case is pending, but BNSF attorneys indicated in court documents that they planned to ask the federal court to consolidate both cases.
In court documents in the Yakima case, BNSF has denied all claims. It said that the allegations are unprecedented and noted that no permit under the Clean Water Act has been issued or required by a regulator for the transport of coal by rail.
The environmental groups cheered Wednesday's news. A message left Wednesday with BNSF wasn't immediately returned.