You can think of waves in matter, whether light waves or sounds waves, as acting on tiny tuning forks.
Light is scattered, reflected, etc, by being re-radiated by atoms. Like with a tuning fork, There's a characteristic frequency, the Natural Frequency, at which the electron in an atom will oscillate ideally leading to less dampening. Other frequencies are absorbed. this gives rise to objects having a characteristic color. Natural Frequency gives color.
A similar principle applies to sound. Materials treat different wavelengths differently in transmission, re-radiation, etc. Strike a tuning fork, its natural freqency yields a characteristic tone.
So as mentioned above, the ear is attuned to certain wave properties in the air, and the air itself propagates sound in a characteristic way.
Water transmits sounds differently, the composite "tuning forks" are stiffer. Then the transfer of the tuning forks of water to the tuning forks of the ear also have a different relation to the air sound relationship.
Paul G. Hewitt's Conceptual Physics has a really good treatment of this in non-mathematical terms.