The colour/transparency of all things is related with how the molecules that form the thing interact with light. When a ray of light hits a molecule, a combination of these three things can happen:
– The light passes through
– The light gets reflected
– The light get absorbed like heat
Water looks transparent because its molecules mostly let the visible light pass trough (mostly, if not water would be invisible!). There are other types of light that the human eye cannot see, like microwave and infra-red light, and water is not so transparent to them. For example, water would absorb most microwave radiation, that is how food gets hot when we put it on a microwave oven!