For one, it’s not perfectly transparent. Totally pure H20 might be, but for the most part there will be some particulate that will absorb light.
Otherwise, even tiny pure water drops can have shadows because of refraction and reflection. The light will bounce off the surface of the drop and be scattered through the middle of it, leaving a shadow on the other side.
Things are seldom, if ever, absolute. This is one of life’s lessons. It is easy to think of things in binary – yes/no, have/don’t have, 0/1, good/bad etc etc. This is simple but misleading. Most things are measured and exist in a spectrum.
Water is transparent enough that we call it “transparent” but that doesn’t mean it doesn’t affect light at all. It absorbs some, it refracts some and at different angles, it reflects some light etc.
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