Which phenomenon of light makes the water to appear shallower than it really is ?
This happens due to refraction.
The reason is that the rays of light reaching you from the object at the bottom of the water do not come straight to you, as they would if there was no water between you and the object. The light travels straight as long as it is in the water, but if it emerges obliquely from the water into the air it is bent downward toward the surface. This bending is known as refraction, and it occurs whenever light passes from one transparent medium into another of different density – as, for example, from water to air, or from air to glass. The eyes do not take refraction into account, but judge the position of the object as if the light came in a straight line.