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Refraction at the water surface gives the "broken pencil" effect shown above. Submerged objects always appear to be shallower than they are because the light from them changes angle at the surface, bending downward toward the water.
As light passes from one transparent medium to another, it changes speed, and bends. How much this happens depends on what it is passing through and the angle of the light ray.
In the diagram, the dark rectangle represents the actual position of a pencil sitting in a bowl of water. The light rectangle represents the apparent position of the pencil. Notice that the end (X) looks like it is at (Y), a position that is considerably shallower than (X). When would it be important to have an understanding of this effect?