The weight of
the water displaced by the hull of a floating boat equals the total weight of
the boat and its contents. This is called "Archimedes Principle", and
is true of any object floating in any fluid.
If stones are removed from the boat, it becomes
lighter and displaces less water. That means it rises up so that less of its
volume is below the surface. The change in the submerged volume of the boat
equals the volume of water weighing the same as the stones removed.
Archimedes principle. If you add 100 kg to the boat, it will displace 100 kg of water. One kg of water is one liter, so 100 kg equals 100 liters displaced, much more than the 1 cc displaced when the marble is thrown overboard.
The same principle applies to stones, but the results would be less dramatic.