The color of water varies with the ambient conditions in which that water is present. While relatively small quantities of water appear to be colorless, pure water has a slight blue color that becomes deeper as the thickness of the observed sample increases. The hue of water is an intrinsic property and is caused by selective absorption and scattering of blue light. Dissolved elements or suspended impurities may give water a different color.

The intrinsic color of liquid water may be demonstrated by looking at a white light source through a long pipe that is filled with purified water and closed at both ends with a transparent window. The light sky blue color is caused by weak absorption in the red part of the visible spectrum.

Absorptions in the visible spectrum are usually attributed to excitations of electronic energy states in matter. Water is a simple three-atom molecule, H₂O, and all its electronic absorptions occur in the ultraviolet region of the electromagnetic spectrum and are therefore not responsible for the color of water in the visible region of the spectrum. The water molecule has three fundamental modes of vibration. Two stretching vibrations of the O–H bonds in the gaseous state of water occur at v₁ = 3650 cm⁻¹ and v₃ = 3755 cm⁻¹. Absorption due to these vibrations occurs in the infrared region of the spectrum. The absorption in the visible spectrum is due mainly to the harmonic v₁ + 3v₃ = 14,318 cm⁻¹, which is equivalent to a wavelength of 698 nm. In liquid state at 20 °C (68 °F) these vibrations are red-shifted by hydrogen bonding, resulting in red absorption at 740 nm, other harmonics such as v₁ + v₂ + 3v₃ giving red absorption at 660 nm. The absorption curve for heavy water (D₂O) is of a similar shape, but is shifted further towards the infrared end of the spectrum, because the vibrational transitions have a lower energy. For this reason, heavy water does not absorb red light and thus large bodies of D₂O would lack the characteristic sky blue of the more commonly found light water (¹H₂O).

Absorption intensity decreases markedly with each successive overtone, resulting in very weak absorption for the third overtone. For this reason, the pipe needs to have a length of a meter or more and the water must be purified by microfiltration to remove any particles that could produce Mie scattering.

Lakes and oceans appear cyan for several reasons. One is that the surface of the water reflects the color of the sky, which ranges from cyan to light azure. It is a common misconception that this reflection is the sole reason bodies of water appear cyan, though it can contribute. This contribution usually makes the body of water appear more a shade of azure rather than cyan depending on how bright the sky is. Water in swimming pools with white-painted sides and bottom will appear cyan, even in indoor pools where there is no sky to be reflected. The deeper the pool, the more intense the cyan color becomes.

Some of the light hitting the surface of the ocean is reflected but most of it penetrates the water surface, interacting with water molecules and other substances in the water. Water molecules can vibrate in three different modes when they interact with light. The red, orange, and yellow wavelengths of light are absorbed so the remaining light seen is composed of green, cyan, and blue wavelengths. This is the main reason the ocean's color is cyan. The relative contribution of reflected skylight and the light scattered back from the depths is strongly dependent on observation angle.

Scattering from suspended particles also plays an important role in the color of lakes and oceans, causing the water to look greener or bluer in different areas. A few tens of meters of water will absorb all light, so without scattering, all bodies of water would appear black. Because most lakes and oceans contain suspended living matter and mineral particles, light from above is scattered and some of it is reflected upwards. Scattering from suspended particles would normally give a white color, as with snow, but because the light first passes through many meters of cyan-colored liquid, the scattered light appears cyan. In extremely pure water—as is found in mountain lakes, where scattering from particles is very low—the scattering from water molecules themselves also contributes a cyan color.

Diffuse sky radiation due to Rayleigh scattering in the atmosphere along one's line of sight gives distant objects a cyan or light azure tint. This is most commonly noticed with distant mountains, but also contributes to the cyanness of the ocean in the distance.^{[citation needed]}