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Q: Why do some colors appear black when they're in the water? I know it has something to do with wavelengths, but I don't really understand it.
A: Water transmits light of every color and, therefore, looks clear. The clearness enables you to see colors of an underwater object near to the surface. Water is clearest for colors of shortest wavelengths%$the blues and greens. That's why water looks greenish-blue and the deeper the water, the more greenish-blue it looks. This effect is most noticeable in the water looking up. Looking down into the water, reflections and refractions on the surface can interfere.
Water isn't perfectly clear, though, especially for colors with longer wavelengths. It strongly absorbs infra-red (heat) radiation and weakly absorbs colors in the red and orange part of the spectrum. White light consists of red light plus its complement, greenish-blue light. So absorbing orange and red colors from white light leaves greenish-blue, the intrinsic color of water.
This also means that orange and red colors in deep water look black if illuminated by surface light. Think what a "red" fish means. The fish looks red, not because it emits red light, but because it reflects red light. If, at depth, there's no red light left, then a red fish will look unlighted or black.
Water molecules absorb red light weakly and infra-red strongly because the molecules vibrate greatly in the infra-red frequencies. They resonate%$that is, they vibrate a greater amount at that frequency like a gong vibrates and "bongs" when hit with a hammer.
The vibrating molecules get hotter due to their motion, like those in a bowl of water warming in the summer's sun.
Occasionally water molecules absorb visible red light. Since the effect is faint, it takes many molecules%$about nine feet of water depth--to absorb enough red light so the blue of the water is noticeable. That's why a glass of water looks clear.
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