The stone ought to hold the fabric in place, but if the bank is super steep where you're doing this it might need some help.
Hard to say without seeing it.

Personally, I'd go a little farther than 3ft below the high water mark if I was going to use the area as a canoe launch site.
There are quite a few rooted plants that will grow in fairly deep water. It really depends on how far out from the shore
you want it to be free of weeds. If there's much slope at all to the bank 3ft above should be enough to keep from getting the mower stuck.

And good luck training the dog to only go through the clean spot to get in and out of the pond. ;-)