The observer is outside the water; the stones are in water (say, 1 m below the surface). This produces a higher-pitched sound for the observer than if both the observer and the stones are in air.
Is this because it takes more energy for the sound waves to travel through water than through air, so that the ones that we hear from outside are the ones that had higher frequencies after the collision to begin with?
Does the density of the medium that is disturbed by a rigid body collision have any effect on the frequency distribution of the sound waves that are generated? For example, does the higher "stiffness" of the cage of water molecules surrounding the stones that are vibrating mean higher frequency normal-modes?
Finally, does the refraction at the water-air interface play any role?