For the same reason that your ears might ache when you take off in a plane: The pressure outside your ear (in this case, water pressure) is greater than the air pressure inside your ear, causing your eardrum to bend painfully inward. Changes in water pressure happen much more rapidly than changes in air pressure, however, and your tears will begin to ache in as little as 5 feet (1.5 m) of water.
In this case, there is water on the outside of this ear drum, but air on the inside. If you don’t do anything, the pressure inside will still be at atmospheric pressure. However, on the outside, the pressure will be greater. This means that the force from the inside air will not cancel with the pressure from the outside. Your ear drum doesn’t want to accelerate, so it stretches like a spring to produces a net force of zero. This stretching of the ear drum hurts.
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