Corals have a phenomenal variety of color and forms; as air breathers, we can't say what they make the nearby region smell or taste like, but if you want, you could consider them to be like an undersea spice-rack - a scent of cinnamon for nearby fire-coral, a bit of mint for the fan coral ect. Light and color also change as you get deeper in depth, more and more of the spectrum is filtered out.
As far as underwater or fantasy weather goes, there can in some areas be large releases of methane hydrates from the ocean floor; this is one theory behind the sudden sinking of ships in the Bermuda triangle, they fall into the bubble. Thermoclines are bands where the temperature of the water can shift very suddenly, going from 'this is cold' to 'numbing' in just a foot or two of depth difference. Cave formations can also have a 'wind tunnel' effect on currents (possibly, opening an underwater door can do the same thing in some circumstances).
One thing that divers can experience is something called Nitrogen Narcosis (basically, you suddenly get 'stoned' or drunk underwater. Very dangerous. Although this might not apply to PCs using magic to breathe, you might work it in as a some kind of fantasy weather effect? Wandering pockets of water that effect as a Confusion spell if a Fort Save is failed.
You might find it useful for some more added realism to check out some PADI scuba training materials if you can find copies cheaply, especially around Deep Diving or Wreck Diving. A large part of the manuals will be safety or gear oriented (always having a backup, constantly monitoring your time underwater and air supply) - but this applies double too for adventuring PC's underwater. Spells have durations - how are they keeping track of them? In an underwater environment, the most lethal spell an opponent might have could be 'Dispel Magic' ;)