First off, the sky is blue because of Rayleigh scattering. Longer wavelengths like red, yellow, and orange pass through, but shorter wavelengths are absorbed by oxygen and other gases and then radiated, hence the blue sky.
Water, on the other hand is very complicated.
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Water has an intrinsic color, and this color has a unique origin. This intrinsic color is easy to see, as can been seen in the Caribbean and Mediterranean Seas and in Colorado mountain lakes. Pure water and ice have a pale blue color, best seen at tropical white-sand beaches and in ice caves in glaciers (green colors are usually derived from algae). It is neither due to light scattering (like the sky), nor dissolved impurities (e.g., Cu2+). Because the absorption which gives water its color is in the red end of the visible spectrum, one sees blue, the complementary color of orange, when observing light that has passed through several meters of water. This color of water can also be seen in snow and ice as an intense blue color scattered back from deep holes in fresh snow.
Water owes its intrinsic blueness to selective absorption in the red part of its visible spectrum. The absorbed photons promote transitions to high overtone and combination states of the nuclear motions of the molecule, i.e. to highly excited vibrations. To our knowledge the intrinsic blueness of water is the only example from nature in which color originates from vibrational transitions. Other materials owe their colors to the interaction of visible light with the electrons of the substances. Their colors may originate from resonant interactions between photons and matter such as absorption, emission, and selective reflection or from non-resonant processes such as Rayleigh scattering, interference, diffraction, or refraction, but in each case, the photons interact primarily or exclusively with electrons. The details of the mechanism by which water is vibrationally colored will be discussed in the paragraphs which follow.
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