Seven environmental groups sued BNSF Railway in 2013, arguing the railroad violated federal law by releasing coal pollutants into waters without a permit.
A federal judge in Seattle on Tuesday found that coal particles that fall into waterways from passing uncovered coal trains are considered "point sources" of pollution and that BNSF would be liable for such pollution if the groups prove at trial that the discharges actually occurred.
Group representatives say they look forward to proving their case about the environmental harms.
BNSF spokeswoman Courtney Wallace said Wednesday the company is confident in its legal arguments and that its coal-loading rule eliminates most coal dust issues.
Hundreds of trains carrying coal from the Powder River Basin in Montana and Wyoming traverse Washington state each year.