Although I've never bow hunted from a water craft, I've done a lot of duck hunting from all three and used a canoe to rifle hunt. I usually transport my weapon in a case to protect it. The one thing I always do is tether either the case or weapon to the boat, canoe, or kayak. In the unfortunate event that you should take a spill in the dark in a swamp, at least your weapon is still attached to your boat. I can only imagine I'd do the same with a bow.
I use a dog leash for the tether. It's soft on the gun and inexpensive. Loop the handle end of the leash either through the case handle or through the trigger guard and around the receiver, and clip the other end to the boat.