If glasses are clear and water is clear, why can you see water in a glass?

Before finding the answer why cay we see water in a glass, let us find the answer why glass is visible even though it is clear.

A transparent material glass is not only allowing the light to pass through it but it reflects some portion of light falling on it.
When we look into a glass fitted to the window, we see the reflected images of objects which are in front of the glass and we also see the objects which are behind the glass. Also we see objects like dust and other material present on both sides of the glass. If the glass plate is perfectly clean, we will have a doubt whether there is a glass or not. In that case only the reflecting property will guide us to decide.
Now remove the glass plate from the panel. Air alone is present.
We are in the air medium and hence there is no question of reflection. Air is transparent and we are not seeing air.
If dust particles are present we see the dust particles in air.
Smoke which is having different refractive index than air makes us distinguish between air and smoke.
Thus mainly the reflecting properties of transparent material guide us to perceive the presence of these materials.

In a lengthy tube whose upper surface and lower surface are not visible and filled with water, we can’t perceive the presence of clear water. However we can perceive the presence of the tube because its surface reflects and the rays coming through the tube from behind are refracted by it.