Environmental groups last July sued BNSF in federal court in Eastern Washington, alleging the trains spilled coal and coal dust into the Columbia River and other waters without a permit and in violation of the federal Clean Water Act.
A similar lawsuit is pending in federal court in Seattle.
BNSF filed motions to dismiss in both cases.
On Thursday, Judge Lonny Suko denied BNSF's motion in the Eastern Washington case. The railway had argued that the coal coming off trains is not a point source of pollution and should not be regulated under the national discharge program.
The judge said it was necessary at this point to allow the groups an opportunity to argue their claims.