I've not taken a canoe on Ellesmere, but have paddled along its coast. That was in the early 1990s and there was little support for doing anything north of Grise Fiord. We chartered out of there to the north then came back to Devon Island and finally into Pond Inlet. You might want to contact the Canadian Outfitter Black Feather to see if they do trips to Ellesmere; I recall seeing something from them about 10 years ago. Ellesmere
No worries about water levels in rivers anywhere in the north, the big concern you will have is getting to the put-in. Of course the ice doesn't go out until late August, if it does go out. It doesn't come easy.
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