Im not sure, but if you are going to use a flash, eg. from 45 degree
angle, a polariser is not going to help, but It may remove the reflections
from the sun if it is bright enough to cause an exposure after using
the flash. Also try having two flashes, one on each side of the camera
at 45 degrees. Is this going to be in a controled environment? if you can
prevent waves from happending, the you probably wont have problems
with reflections using the flash.

I have taken photos in a rockpool withing the single flash method
above and works okay. I use digital though, so I can see the
results immediately. Ripples from waves are the main problem.
Also, refraction due to photographing through the water on an
angle causes chromatic abberations as well.

The only other alternative is to go underwater using a housing, or
put them into a tank. Using a tank, you should also using the same
technique with the flash.

Hope this helps

Vin.

Here's a link to some I shot for a magazine

http://www.gregblankphoto.com/gregspublished.html

Bottom of the page in the center, I used Kodak 100VS
no flash no polorizer, between 13:00 & 15:00. You just
need to watch the fish for when they are close to the surface.
Bracket the exposure somewhat and take meter reading from something
standard like a grey card or your hand.

I think its better if the sun is directly over head or slightly off to one side
of overhead,....no long shadows. Mid day is better in this case.
Without the flash your response time will be faster.