same here. i cant fill up an empty canteen in/from a lake

I can refill water bottles and canteens at both water pumps and ponds, and have done so many times. Often you may find it hard to find that sweet spot. I found the best way to fill up a bottle or canteen is to do the following:

1. Get the empty bottle/canteen in your hand
2. Scroll mouse button whilst looking at the source of water, changing your position.
3. Stop when you see an option to refill bottle/canteen and scroll to it then press your action key(f)

So can I, no problem this far while refilling water bottles or canteens. Switching to 1st person view can be helpful also.