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