Why does reflection occur on transparent materials?
It is a property of waves that when they meet an interface, where the medium through which they travel changes, some of the wave is reflected from the interface and some of the wave is transmitted through the interface.
In the case of light it is a change in the refractive index (related to the speed of light in the medium) which produces a reflected and a transmitted wave.
All other things being equal a greater amount of reflection occurs at an air/glass interface than at an air/water interface because the difference in refractive index at the air(n=1)/glass(n=1.5) interface is greater than for the air(n=1)/water(n=1.33) interface.
Note that a light wave traveling in a medium of higher refractive index than the refractive index of the medium on the other side of the interface can be totally internally reflected if the angle of incidence exceeds the critical angle.
In terms of what happens on the molecular scale the incident light waves produces currents (oscillating charges) in the medium and these oscillating charges re-radiate the electromagnetic waves in all directions which add together to form a transmitted wave and a reflected wave.
Richard Feynman has produced a novel way of determining the fraction of light which is reflected in Volume 1 Section 33 of Feynman Lectures in Physics..
As a general answer, waves reflect at discontinuities in the velocity of propagation. This is also true for a pulse on a string, for example at a knot where ropes of different densities are joined together. Or at a mass that is fixed on the string.
Reflection usually happens because of a change in refractive index. Reflection occurs because the EM field of the incoming radiation causes oscillations. Electrons in the material receiving light jiggle as it hits them, making them each secondary emitters of radiation and they re-emit light (effectively seems like bouncing off). Glass and water both have different refractive indices than air, so when there's an interface between air and water or between air and glass, you get a reflection. This is why you see reflections off glass or off the water, or other materials that are normally transparent. This emitted radiation goes both into the substrate and back into the original medium, with the net sum of all of the secondary emissions forming the reflected and refracted rays, respectively.