The district says aggressive deer are a threat to public safety, but the Invermere Deer Protection Society was arguing the town's council did not consult the community before going ahead with plans to destroy 19 deer two years ago.
Devin Kazakoff, head of the deer protection society, called the court's decision disappointing.
"They've agreed with the district on the fact that they consulted the public. We don't agree with the judge's decision, but that's what it is," he said.
Other B.C. communities had been watching this case closely because they use the same public process as Invermere to obtain permits from the provincial government to destroy deer.
Invermere Mayor Gary Taft said the lawsuit was one of the "nastiest experiences I've ever had," and that he and his council received petitions, emails from all over the world and even death threats throughout the case.
"We're glad to have that over with," he said.
The issue of a deer cull in Invermere is not entirely settled, however. A public referendum on Nov. 2 will allow residents to decide if more permits for future culls should be sought by the district.
Kazakoff said he's confident the vote will vindicate his group's efforts.
"You get a few people that think they're aggressive of think they're a nuisance, but generally from the people I talk to... everybody loves the deer. I just hope that shows up in the vote," he told CBC News.Suggest a correction