Jeff, I don't know any tonneau cover that claims to be 100% water proof. Most will claim to protect your items from the elements but not guarantee that some water might get into the bed. Just remember that the more pieces, hinges, seams or seals there are, the more potential leak points.
Much of the water-resistance comes from proper installation, but, over time, even properly installed covers can have the seals deteriorate and start to leak....some faster than others.
The other problem is if you open the cover after a rain...water that was kept out when the cover was closed can drip into the bed and now who is to say that the leak occurred before or after the cover was opened?
...Richard