A bit of background - my parents moved to Canada's Northwest Territories in 1971, and spent three years there as teachers in Fort Providence and Fort Resolution. I was born in the summer while they were down south again, but I spent most of the first year of my life in Fort Resolution. So I'm interested in how these locations came about.
With the Inuit being nomadic (as far as I know), it seems likely that these locations were chosen purely by the Europeans. But maybe they were previously selected by the Inuit as known fishing areas or something like that.
Edit: I mistakenly said Inuit throughout when I should have said Dene. Same question though.
It isn't quite in Canada, but Ft. Yukon, Alaska is an integral part of this story, as the farthest-west Hudson's Bay Co. outpost, actually located slightly within the boundaries of Russian North America. It was founded by a Bay Co. agent in 1847, at a river confluence (the Porcupine and Yukon) that only became significant to Native Alaskans after the fact, when it became an established trading post (furs in exchange for kettles, rifles and other trade goods). Here is some background, including obligatory mosquito references.
Based purely on my own time in the region (14 years) I would say that there really aren't a lot of geographical locations that would have had any practical special interest for Alaska Natives, prior to white contact. Caribou go where they go, and one spot on the Yukon is pretty much as good as any other spot when you are setting up a fish ladder. After contact and conversion to Christianity, of course, a settled town with a church and trading post would change nomadic relations to semi-nomadic, or even settled, patterns.