Top down picture taking help

Other than getting really close to the water, preferably straight down, don't know.
 
Oh. Now I get it. You want to be able to take a larger photo from a few inches above the tank to capture more corals, but with these boxes, you have to break the surface of the water.

This may be a dumb idea, but I built a portable LED light in the past to illuminate specific corals with all the actual lights off. Maybe you can do something similar, but for the whole tank.

For example, turn off the tank lights above and place the "portable" or "Camera" light on the front glass. This should give you no reflection from above and good coral colors.

This is the one I built, but you may need something more powerful.

IMG_20130824_180007.jpg
 
Also, maybe you could build something like the picture below, but larger to hang it in front of the tank while you take pictures.

image_preview
 
not with a direct shot since the light is in the exact same line. It's either a lookdown or illuminate the tank from another angle. or maybe you could do a series of lookdown shots and paste together.
 
Tilt the lights so they don't point the water but still give you light for the fluorescent effect. You can also try using a white sheet attached to the light and the other end hangs behind the tank (in a diagonal), it has to be the right thickness so the bulbs/led don't show but the light passes through for the fluorescent effect.
 
If you have a camera that has a threaded lens, get a polarizing filter. Left image has it, right does not. Won't eliminate direct reflections (bulb), but will reduce greatly. You'll just have to adjust your angle and/or zoom more if that's the case.
 

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get a polarizing filter.
I was just wondering about this.
I'd think, just as you said, the reflections would be decreased. Not sure how much though. I'll see if I can do a little experiment later and post up the pics.
 
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