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' ;) And if you want to see some PCs scurrying away from an underwater fantasy weather effect? A dispel-magic storm underwater will certainly do the trick.
Here's a youtube of a real life ice-column related effect that would be fun to incorporate a fantasy version of as well: http://www.youtube.com/watch?v=r4cX2EPt2zE
Side note - I think that magical water breathing spells protect from pressure differences and changes, but I can tell you that even aside from the dangers of the bends on ascent, just equalizing pressure in your ears can be painful whether you go up or down. If you put a limit on the spell protection, such as 'you can go up or down no more than 10 feet per round without experiencing d6 damage per extra 10 feet', you may find it adds some more flavor, a little more realism, and allows for 'vertical current' weather conditions that would be significant challenges.