The White Pass and Yukon Route Railway has withdrawn its application to use herbicide on its tracks.
The railway is under orders to clear weeds from its tracks because they can weaken the roadbed and make track inspections difficult.
It had submitted an application to use VisionMax and Arsenal, two herbicides which are potentially toxic to aquatic life.
In a letter to Environment Yukon, dated June 30, the railway said it would be within its rights to use herbicide, but that it had been made aware of alternative, non-herbicide methods that may do the job.
"As a community member we would be remiss if we did not examine and test these methods in a attempt to find a solution more acceptable to all involved," said the letter.
Yukon Conservation Society director Lewis Rifkind calls the decision a victory for the environment, "which doesn't happen often these days," he said.
"However we do recognize that these weeds have to be removed and we hope that the railway can find an environmentally friendly or benign way to do that."
So far the railway hasn't said what it plans to do instead.