The water bottle xylophone is played by a person striking bottles filled with different amounts of water there. The bottles are filled to specific amounts so that the waves change distance they have to travel to crash in the water. You change the notes by striking a different bottle. The note is formed when the striking of the object against the bottle shoots into the container and takes a set amount of time to disrupt the water in the bottle producing a different note. This makes me think that sound is changed and produce by sound waves interacting with a medium of different distances and tensions in order to create the unique sound. I think you can conclude that with a longer distance for the wave to travel the deeper the sound will be because the more spread out the wave will be at the point of impact.
Similar to my instrument: http://www.youtube.com/watch?v=Hvquq1kg-lQ