Katrina Bluetchen with Alberta Environment and Sustainable Resource Development says most of the rail cars from the CP train, as well as debris, have been removed from 40 Mile Creek.
Bluetchen says the focus now is on clearing the leaked material from the shore of the creek, which flows into the Bow River.
Fifteen cars on the train left the tracks early Friday morning carrying lentils and fly ash, an ingredient in concrete.
A spokesman with the Transportation Safety Board says neither are hazardous, but Bluetchen has noted there is concern the fly ash could alter the water's pH or pile up as sediment.
The railway says in an email that it is working with Parks Canada and other environmental authorities to ensure the cleanup and any necessary remediation in the area is "timely and appropriate."
"CP regrets any inconvenience to the citizens of Banff and visitors as the work is finished," the email states.
The railway said it is repairing the track and bridge, and that it expected to reopen the section to traffic sometime overnight between Saturday and Sunday.
Bluetchen noted CP must produce daily reports and plans, as well as work with the province and Parks Canada to make sure it meets Alberta requirements.
She said provincial staff would likely be leaving the area on Sunday. Environment Canada, she said, was the lead agency on the case.
No one from Environment Canada could be reached for comment on Saturday.
The Transportation Safety Board is investigating the cause of the crash.