Crown attorney John Cliffe said the Yellowknife prosecutor's office and Fisheries and Oceans Department staff were disappointed with Justice Ted Richard's decision.
Cliffe said case did prove that the Fisheries Act is applicable to all waters, no matter their size, as long as fish are present.
"That's an important finding," he said. "It signals to industry that their operations, whether you're a diamond mine, a road crew or a pipeline construction company, you have to be aware of the environment, especially the aquatic environment."
"This in no way weakens the Fisheries Act. In fact one could argue that it is clarified."
Kevin O'Reilly of the Canadian Arctic Resources Committee said he's disappointed with the decision not to appeal.
"I know it was a long trial and so on but I'm a bit disappointed that the Crown doesn't see fit to follow up and ensure the public interest is protected."