What i do is hunt .png images of what I need then convert them to black and make the image negative, then save as a transparency file. That way I can put them on a plane and tada instant reef. The same thing goes for particles although there's usually no need for a transparency map since the particle maps are usually black and white. I generally parent those to the camera. Oh and the wavy lines...transparency map and a spotlight...or Daz's advanced spotlight which comes with one. FYI For the particles I like to use 4 planes at increasing distances but sized so they fit the viewing area of the camera....then I parent them to the camera. Like in my next image.

I got around the wavy lights and god rays by trying to go deeper than the natural light would be able to penetrate. You do awesome with the water scenes. I too would like a good coral reef set. Another reason I try to avoid the watery lights is from what I mentioned earlier iRay/3Delight.

I actually love doing underwater scenes, they're such a challenge to get right. You must never forget the particles of whatever, the godrays, or the wavy lights. Everything else is gravy you don't need plants but they look awesome, and don't forget the fish...I wish I had more of them. What would be nice is if I had some schools of fish to include for added realism. Or some nice reefs.

Awesome work!